The server is supposed to be in 2.0.3 state in terms of content, but since the the zone is going to have Mudsprocket and other 2.3 patch environment changes anyway, I believe it makes sense to stick with the new improved zone and I'm reporting issues from this perspective.
Mobs
Noxious Flayer should have poison, Noxious Shredder should have Poison and Trash
Darkfang Venomspitter should have Toxic Spit
Consumed Alive ability of Risen Husks should show and play the blood splatter effect
Darkmist spiders don't seem to have their abilities: Recluse (Debilitating Poison), Silkspinner (Poison, Web), Spider (Poison), Widow (Hatch Spiderlings)
Razorspine is supposed to patrol the hill up and down.
Mirefin Oracles don't seem to use their abilities (Lightning Bolt, Healing Wave), neither do Muckdwellers (Creeping Mold)
Grimtotem Breakers don't seem to have their Bone Breaker ability. Spirit-Shifters don't have Shock and Summon Spirit Wolf. Grimtotem Elders don't have Healing Wave and Lightning Bolt. Earthbinders should have Earthbind totem. Destroyers don't have War Stomp. For these mobs I'm going with retail Wowhead information as they aren't included in Bestiary, but they seem to be the same in WotLK databases (like Openwow) as well and are generally a part of content that seems to have not changed.
Darkfang Creepers don't have Slowing Poison, Darkfang Venomspitters should have Toxic Spit
Drywallow Daggermaws don't seem to have Pierce Armor, Snappers seem to be missing Vicious Bite.
Acidic Swamp Oozes don't have their Bubbling Ooze and Rancid Blood abilities, Bubbling Swamp Oozes lack Bubbling Ooze
Firemane Dragonkin don't seem to have their abilities: Ash Tail (Fire Shield, Fire Nova), Scouts (Dual Wield, Fire Shield), Scalebanes (Fire Shield, Sunder Armor, probably Shield Bash), Flamecallers (Fire Shield, Rain of Fire, Fireball)
Searing Whelps and Hatchlings are missing their Flame Spit and Fireball abilities respectively. In addition, they hit outrageously hard, around 200 against mail (mobs at similar level generally hit for around 50 against same armor)
Overlord Mok'Morokk doesn't seem to have his Wide Swipe ability.
Gavin Greyshield fights with his fists, screenshots show a weapon and a shield.
Talking to Jaina offers the dialogue she should have after finishing the Missing Diplomat chain. Luckily, Wowpedia has a detailed list of her dialogue from all stages of the game.
Quests
With Reflective Dust applied to you after handing in Inspecting the Ruins, you can see an imp where Paval Reethe's badge is.
In The Black Shield, Acidic Venom Sacs can be looted from other spiders than the Darkmist Spiders mentioned in the quest.
In "What's Haunting Witch Hill?", you can talk to Restless Apparation as many times you like and instantly get credit for the quest. Indeed, you shouldn't need to talk to the Apparations, they should tell their information as the mobs are killed and then fade soon after (currently they stick around for a good while and die accompanied with human death noise). That's certainly how it was in MoP and the quest likely has remained unchanged in regards to these details.
Marsh Frog Legs don't seem to drop from Giant Marsh Frogs and as such the quest is uncompletable.
In Cleansing Witch Hill, Zelfrax simply appears at the end of dock (and in the ground, such that he has to go around to path to the player who has set up the torch on the dock) without associated effects and RP text. This video displays the quest. Coincidentally, it also shows an RP event happening between Jarl and Grimsby.
The fifth part of "The Black Shield" shouldn't be available until you have completed Questioning Reethe and Suspicious Hoofprints: "After completing all three quest chains, Krog will offer a fifth The Black Shield quest, asking players to bring the Blackened Iron Shield to Mosarn (55.6,79.6) in Thunder Bluff." (Wowhead)
Questioning Reethe RP is handled really clumsily after the interruption of Alliance soldiers, this video shows the event
As you hand in Suspicious Hoofprints, an NPC spawns and is sent to investigate. For Horde it's Kagoro, for Alliance it's Falgran Hastil. Videos of Horde and Alliance versions of the event.
In Twilight of the Dawn Runner, the captive NPC Ithania is killed by the mobs surrounding her and when talked to, she just says "Greetings " (the correct text and behaviour, escaping from the tower, is shown in this video).
The escort event in "Stinky's Escape" doesn't start. It's worth noting that there's an Alliance and Horde versions of the quest but they should be identical aside from where you hand the quest in.
In The Grimtotem Weapon, the captured totem doesn't generate the debuff upon nearby units that allows you to get quest credit for killing Mottled Crocolisks.
In "Raze Direhorn Post!", the tents aren't set ablaze as you use the quest item and you need to be inside to use the quest item, pretty deep at that in two of the cases.
Currently, you get credit for Corrosion Prevention from just talking to the NPC repeatedly. Makes sense, as the energy charges from Power Core fragments and quest item don't work and you couldn't get credit legitimitely.
The ogre spirits in Spirits of Stonemaul don't say anything. In addition, while I was checking the dialogue, turns out there's also a spell effect upon summoning them and while I don't remember such a thing, it likely existed in 2.3 already.
Challenge to the Black Flight becomes available as you complete Bloodfen Feathers. While I can't find direct evidence of quest order, as you use the banner acquired during Banner of Stonemaul, it should go without saying that it needs to be done first, and The Essence of Enmity likely has to be done also.
During quest Challenge Overlord Mok'Morokk, the ogre cannot be attacked, making the quest uncompletable through legitimate means. If he was attackable, the quest also requires credit for killing him, which it shouldn't (and as he runs away before being killed, receiving credit would be impossible). In addition, as I accepted the quest, he did a really weird detour away from his current position before engaging. As I defeated him, he also ran to his spawn location first and stayed there for a while before actually running away proper.
In The Essence of Enmity, you can get credit multiple times from the same corpse (the corpses shouldn't disappear, though, you can skin the mobs after using the totem).
You are prone to being stuck inside the banner you planted in Challenge to Black Flight (I did it several times, got stuck about half on the attempts, might be related to not moving away as the cast is finished but this clearly shouldn't happen). In addition, there's no RP (the Smolderwring should cry "Pitiful Mortal! Onyxia answers to no one!" and "Your pathetic challenge hasn't gone unnoticed. I shall enjoy toying with you before you die." before charging forth and burning the banner, then becoming attackable.
As this is the zone the chain ultimately leads to, I'm reporting the issue here. During The Missing Diplomat, Dashel Stonefist doesn't have dialogue for when he attacks and is defeated, and the thugs don't attack you unless you go to aggro them. You can see the correct behaviour in this video. The follow-up is also missing that kind of details (no text, follows despawn immediately rather than soon after). In addition, he is green until reaching his destination (should be yellow), runs towards his friends rather than his friends running to assist him, and most importantly, he turns green after being "defeated" but doesn't stop attacking. Indeed, the quest seems to require killing him for whatever reason, which would render the quest impossible to complete.
In Traitos Among Us you get credit for merely right clicking the Deserter Agitators. On the other hand, the dialogue option does nothing. Wowpedia lists the possible outcomes. In addition, the dialogue option doesn't disappear as you complete the quest.
Propaganda War doesn't have the brief RP event upon handing it in.
Besides the mage tower at Theramore, Archmage Tervosh should also be able to appear inside Sentry Point. If you read the quest text, this should be fairly obvious ("is not here [Sentry Point]"). Indeed, looking at this video, he teleports to the tower as you enter it. According to Wowhead comments, looks like there's only one Tervosh and he teleports around, returning to the mage tower pretty quickly afterwards he's been summoned by one of the questing players (either at this or the final part of the quest). In addition, he should cast Proudmoore's Defense upon completing the quest.
The RP from the final confrontation is also missing. As you can see, the guards don't aggro, some dialogue is missing, he isn't imprisoned in a bubble and Jaina with her gang doesn't show up. And of course, you should be able to hand the quest in to the mage and get the final part for the ring from Jaina at the spot. About a minute after, Jaina teleports out (and as mentioned in the mob section, Jaina's dialogue changes as you complete the chain).
Judging by the video the final and 17th part quest should be given by Jaina. In addition, it lacks the quest text.
Upon handing in the Orc report, you don't get the follow-up. There's a few mutually exclusive quests that lead you to Foothold Citadel (They Call Him Smiling Jim Quest Complete and such like) but I didn't find any evidence of this being one of them and it certainly wouldn't make sense as it's not related to Shady Rest Inn. In addition, Wowwiki mentioned an RP scene that plays out as you hand in the quest and Wowhead mentions a further Discworld tribute during the event. This video seems to show the event (minus the salute, as the player is a cat) which seems to have remained intact in retail.
During Recover the Cargo!, debris doesn't disappear as you salvage it, allowing you to credit in one spot.
The flight route in Survey Alcaz Island doesn't work, rendering the quest impossible.
Jaina isn't able to teleport you in Warn Bolvar!. In addition, in the follow-up, Archmage Malin cannot teleport you to Theramore (keeping the quest was a commonly used shortcut). Details of the interaction can be found in Wowwiki.
"Take Down Tethyr!" autocompletes. This video shows the event.
In Unleash the Raptors, using the quest item places it on the ground but nothing happens and you don't receive credit. This video shows the raptor attack.
In The Deserters, Balos Jacken doesn't turn green as you beat him up (according to Wowpedia, he should say " Alright! Alright! We surrender... Just put your weapons down, I'll cooperate!").
For whatever reason, as I handed in Justice for the Hyals, I got "Quest accepted: Peace at Last" in my chat log but received the error sound and no quest. Vimes doesn't offer the quest either, relog did nothing for that. I was level 40 so I don't know what could possibly be the problem. In addition, the RP scene is missing. Lynn Hyal spawns and you can talk to her, but she only says "Greetings " and the quest completes. Instead, an RP scene is supposed to play out with credit received after you've watched it. The quest seems to have remained unchanged, this is how it's in retail.
The server is supposed to be in 2.0.3 state in terms of content, but since the the zone is going to have Mudsprocket and other 2.3 patch environment changes anyway, I believe it makes sense to stick with the new improved zone and I'm reporting issues from this perspective.
Mobs
Quests