There are Whirling Invaders despite elemental invasions seemingly being unimplemented
Stonelasher Scorpid doesn't seem to use Venom Sting, Pincers seem to miss Venom Sting and Tendon Rip, Flayers seem to lack Thrash and Vemon Sting
Sand Scitterer doesn't seem to have poison, Rock Stalkers seem to lack Poison and Web
Dredge Strikers were infamous for stunning charge which they don't have. Crushers also seem to miss their Lash ability.
Mobs at Southwind Village don't appear in Bestiary either, although Tortured druids at least certainly should use abilities. Both Valkyrie database and retail Wowhead list very much plausible Moonfire, Healing Touch and Summon Hive'Ashi Drones, which Sentinels also have.
Sillithid in the big hives were elite prior to 2.3. In addition, Hive'Ashi Defender lacks Disarm. Hive'Regal Hive Lord seems to lack Berserker Charge. Spitfire seems to lack Corrosive Acid Spit and Swoop, Ambusher seems to lack Poison. Hive'Zorah Hive Sisters seem to lack Toxic Spit. Reavers don't have Cleave and Knockdown. Wasps seem to lack Poison.
Twilight cultists have missing abilities. Avengers are missing Enrage, Geolords Boulder and possibly Earth Shock (the AI retail might only have cast it to interrupt, though). Stonecallers lack Summon Earth Elemental, Petrify and Fireball. Twilight Masters don't have Chain Lightning, Frost Nova, Fire Blast and Frostbolt, Overlords miss the exact same abilities. Flamereavers lack Immolate.
Rare spider Gretheer lacks abilities (Deadly Poison and Web)
Cenarion Scout Jalia isn't stealthed. Same with Azenel, who also lacks proper dialogue (Greetings ).
Twilight Keeper Havunth lacks Fire Blast and Fire Nova. Mayna probably lacks Psychic Scream, Mind Flay and Shadow Word: Pain (I accidentally killed her very quickly). Evenrun doesn't have Shadow Shock or Fireball. Exeter doesn't have Consussion Blow or Mortal Strike.
Rare mob Setis doesn't have any abilities either (Crowd Pummel, War Stomp).
You can't finish your discussion with Ralo'shan the Eternal Watcher (whole discussion in the link, it's post-Cata but all previous lines seem to match so I'd imagine the last one has remained unchanged as well).
Mistress Natalia Mar'alith doesn't have her abilities (Greater Heal, Blackout, Mind Flay, Psychic Scream, Shadow Word: Pain). In addition, she should have some dialogue.
Quests
In Hive in the Tower, you can't interact with the pod (and thus spawn mobs that would drop the quest item), rendering the quest impossible to complete.
In Field Duty you are ought to defeat an elite mob before you can get your papers signed. I'm not going to look into those on case-by-case basis, but it's worth noting some of the assignments (and possibly the attack events as well?) were nerfed in 2.3 patch.
As described in #2146, quest Scouring the Desert cannot be completed.
The repeatable Encrypted Twilight Texts quest gives a thousand reputation. According to comments in Wowhead, it gave 250rep prior to 2.2 when it was buffed to 500rep.
Scrying Materials doesn't have progression and completion quest text, same with Grinding Stones for the Guard, Desert Survival Kit. All of the logistics assignment quests, actually. I think one of the Combat Missions had the same issue (I handed all the 12 quests in bulk and just barely caught a glimpse of missing text and had already moved on before taking note of which quest it was).
I didn't pay attention while doing the quests, but looking at my chat log, some of the assignment quests appear not to have rewarded any reputation (they should reward 150).
I once encountered follow-up Logistics Assignment letter that contained two follow-up assignments (rewarded from one of the initial quests). To my knowledge there should only ever be one follow-up assignment. In addition, one of the Followup Tactical Assignments was empty.
After having completed Grinding Stones for the Guard once, trying to start it a second time gives "You are already on the quest" error message. Applies for "Earthern Templar" as well, possibly some other quests.
Allegiance to Cenarion Circle provided 2000 rep. According to Wowhead it should be 500 in 2.0 patch. Brann Bronzebeard's Lost Letter also seemed to provide double rep. Braan'z Letter also keeps on dropping even after having completed quest.
In Glyph Chasing, interacting with the crystals simply gives "Greetings " response, preventing rubbing from being made and rendering the quest impossible. It's post-Cata, but this video shows the relevant dialogue and while post-Cata version only requires one rubbing, the quest seems otherwise unchanged.
The Calling works inadequately. Firstly, it was a raid quest prior to 2.3 during which it was dropped to group quest status. In addition, the Three Sillithid (Aluntir, Arakis and Xil'xix) didn't spawn before him. The Emissary didn't have any abilities. The RPevent from handing in the quest didn't play out as you hand in the quest. And while I can't find information on this, for me it would seem really weird for the whole event at the dragon skeleton to lack any RP. This video shows something (the bug spawns before Roman'Khan). The reputation for this quest also seems to be double (received 1400, Wowwiki says 700).
Scout reports for Tactical assignments seem to be impossible, as you don't get the report from interacting with the scouts.
General
2146
There's several of Brood of Nozdormu in Silithus. As you approach them, it's quite common for them to appear in the ground and until then receive the correct vertical position. They also seem to be stationary.
The whole Windstone interaction component is missing. For starters, Twilight Trappings don't seem to drop. Even if you wear a full set, interacting with Lesser and Greater Wind Stones displays "Greetings " rather than allowing you to summon one of the mobs. This makes a number of quests, be it "Earthern Templar", "Lords of the Council" and so forth impossible to complete. And let's not even think of Crests of Beckoning or other final details of the summon system.
Mobs
Quests
General
2146