After discussing it with a few people of the server I compiled all my separate posts into one for a total overview.
During my hunt for the Loremaster title this is what I came across in Northrend as Horde. Without some of these quest chains Loremaster of Northrend is unachievable.
The Dead Rise:
Orfus of Kamagua The quest-giver doesn't have the exclamation mark (!) above him so big part of the quest-line towards the achievement falls away.
A Fall From Grace:
The quest could be completed in the quest log but can't be deliver to the quest giver Agent Skully (says continue but when you click it nothing happens).
Magic Carpet Ride:
Talked to Yanni for the ride, Get mounted on carpet, doesn't auto-fly and have to fly yourself. When reaching the quest point at Previous known as Gorge the Corpsegrinder now Annihilator Grek'lor You can't deliver the quest.
Pa-troll:
Can't be completed by multiple fractions from Commander Kunz can't be completed (I assume also all the daily versions won't work, If I have to post all those it will be a really long post).
The Lok'lira's Bargain keeps phasing in and out in Brunnhildar Village that you have to leave village and come back.
Krolmir, Hammer of Storms:
When going trough the dialog of King Jokkum You mount on him but he doesn't bring you to the quest spot. When you travel there yourself no further dialog and/or Thorim there for the follow-up quest.
Changing the Wind's Course:
When using The Lorehammer It spawns Stormhoof but doesn't put you in his shoes to attack The North Wind to get the Horn of Elemental Fury After spawning like 100's of Stormhoof's I found out that you can put yourself in his shoes in the cave (The Howling Hollow) behind "The Plain Echoes" (as the quest describes). That is a pretty misplaced location.
Into The Wild Green Yonder:
Mounted on the protodrake but can't rescue Captured Crusader Rescuer when clicking on the "Grab Captured Crusader"
After further testing I could just hoover above the rescue spot and spam the drop off button and it counted without having to leave the area.
After discussing it with a few people of the server I compiled all my separate posts into one for a total overview.
During my hunt for the Loremaster title this is what I came across in Northrend as Horde. Without some of these quest chains Loremaster of Northrend is unachievable.
Howling Fjord I've Toured the Fjord
Warning: Some Assembly Required: When you explode the Abomination it doesn't count towards the quest.
The Dead Rise: Orfus of Kamagua The quest-giver doesn't have the exclamation mark (!) above him so big part of the quest-line towards the achievement falls away.
Forgotten Treasure: Handsome Terry Same as Orfus doesn't give the exclamation mark (!).
Spirit of the ice: Lurielle Same as Orfus and Handsome Terry doesn't give the exclamation mark (!).
Dragonblight Might of Dragonblight
A Fall From Grace: The quest could be completed in the quest log but can't be deliver to the quest giver Agent Skully (says continue but when you click it nothing happens).
One of a Kind!: The exclamation mark (!) doesn't show up above Aurastrasza.
Mystery of the Infinite, Redux: Chromie gives the quest plus item, When the item Hourglass of Eternity Gets placed, nothing happens (tried 3 times).
Report to Lord Devrestrasz: The exclamation mark (!) doesn't show up above Alexstrasza the Life-Binder.
Imbeciles Abound!: The exclamation mark (!) doesn't show up above Doctor Sintar Malefious.
The Kor'kron Vanguard!: The exclamation mark (!) doesn't show up after completing all previous quests above Overlord Agmar.
Borean Tundra Nothing Boring About Borean
Taking Back Mightstone Quarry: The question mark (!)doesn't show up above Overlord Razgor.
Magic Carpet Ride: Talked to Yanni for the ride, Get mounted on carpet, doesn't auto-fly and have to fly yourself. When reaching the quest point at Previous known as Gorge the Corpsegrinder now Annihilator Grek'lor You can't deliver the quest.
Bring 'Em Back Alive: You can jump on the kodo but not move them back to the quest giver Farmer Torp.
Nork Bloodfrenzy's Charge: Garrosh Hellscream doesn't have exclamation mark (!) after the required quests are done.
Karuk's Oath: Karuk has no exclamation mark (!) above him.
Prison Break: Librarian Donathan has no exclamation mark (!) above him.
Learning to Communicate: King Mrgl-Mrgl doesn't have exclamation mark (!) above him.
Escape from the Winterfin Caverns: Walk with Lurgglbr till the end point, there he just de-spawns and not getting marked as complete.
Kaganishu: When using Kaganishu's Fetish on Farseer Grimwalker's Spirit it doesn't set him free thus can't be completed.
Across Transborea: Taunka'le Evacuee follows you, but can't deliver quest at Wartook Iceborn since it doesn't give complete credit.
Grizzly Hills Fo' Grizzle My Shizzle
Filling the cages : Samir doesn't have an exclamation mark (!) after delivering Good troll hunting.
Ruunas Request: Ruuna the Blind doesn't have an exclamation mark (!) after delivering https://www.wowhead.com/wotlk/quest=12425/ruuna-the-blind.
The Horse Hollerer: Throwing Flashbang Grenade at the Mustangs, they don't run away frightened.
Raining Down Destruction: Kurun doesn't have an exclamation mark (!) after delivering An Expedient Ally. It did work after a gm gave the alliance version Find Kurun.
Rallying the Troops: Again Kurun doesn't have an exclamation mark(!) after completing Raining Down Destruction. Maybe they linked wrong somewhere because different faction?
Zul'DrakThe Empire of Zul'Drak
Infiltrating Voltarus: Stefan Vadu doesn't have an exclamation mark (!) after completing Dressing Down.
That's What Friends Are For: Gerk found but it doesn't make it complete in the log or at Crusader MacKellar.
Light Won't Grant me Vengeance: Gerk doesn't have the exclamation mark (!).
Getting the quest So Far So Bad from Stefan Vadu (Side issue: didn't work on his dragon so had to go to Ebon Watch) doesn't give me the Overlord Drakuru task It Rolls Downhill.
Hazardous Materials: Same issue, Overlord Drakuru doesn't give the task Zero Tolerance.
Sabotage: Use Explosive Charges, Blows up the wagon doesn't give credit and again the same issue, Overlord Drakuru doesn't give the task Fuel for the Fire thus not being able to do the quest Disclosure after to complete Sabotage.
The Key of Warlord Zol'Maz: You can summon Warlord Zol'maz but he is not attackable.
Pa-troll: Can't be completed by multiple fractions from Commander Kunz can't be completed (I assume also all the daily versions won't work, If I have to post all those it will be a really long post).
Captain Brandon doesn't have quest Something For The Pain for Pa-troll.
Captain Grondel doesn't have quest Creature Comforts for Pa-troll.
Alchemist Finklestein doesn't have quest Lab Work for Pa-troll.
Sholazar Basin Into the Basin
The Mist Isn't Listening: The npc's (Mistwhisper Gorloc) you need to kill are invalid when you want to attack.
Forced Hand: The npc's (6x Frenzyheart Scavenger and 8x Frenzyheart Spearbearer) you need to kill are invalid when you want to attack.
Frenzyheart Tribe Daily's:
Tools of War: Sparktouched Gorloc are un-attackable.
Kartak's Rampage: Sparktouched Gorloc slain are un-attackable.
Secret Strength of the Frenzyheart: Sparktouched Gorloc are un-attackable.
The Oracles Daily's:
Will of the Titans: Frenzyheart Attacker are un-attackable.
Power of the Great Ones: Frenzyheart Attacker un-attackable.
Mastery of the Crystals: Frenzyheart Attacker un-attackable.
Song if Fecundity: There are no Soak Fertile Dirt spawns.
Storm Peaks The Summit of Storm Peaks
The Lok'lira's Bargain keeps phasing in and out in Brunnhildar Village that you have to leave village and come back.
Krolmir, Hammer of Storms: When going trough the dialog of King Jokkum You mount on him but he doesn't bring you to the quest spot. When you travel there yourself no further dialog and/or Thorim there for the follow-up quest.
Sniffing Out the Perpetrator: When you mount the Frost Saber, It doesn't auto walk and doesn't have attacks/get attacked. When at the location Tracker Thulin doesn't spawn to give Brann's Communicator by loot.
Changing the Wind's Course: When using The Lorehammer It spawns Stormhoof but doesn't put you in his shoes to attack The North Wind to get the Horn of Elemental Fury After spawning like 100's of Stormhoof's I found out that you can put yourself in his shoes in the cave (The Howling Hollow) behind "The Plain Echoes" (as the quest describes). That is a pretty misplaced location.
Cold Hearted: You can deliver Rescued Brunnhildar Prisoners but it doesn't count for Freed Proto-Drakes. Also you have to fly yourself and not auto fly once you leave Dun Niffelem.
Quest Battling the Elements: Can't be completed since there are no snow bumps to pick up.
The Sons of Hodir Daily's.
Quest (daily) Feeding Arngrim: Can't be completed since Roaming Jormungar don't get the debuff.
Quest Thrusting Hodir's Spear and the daily How To Slay Your Dragon: Can't be completed since Wild Wyrm Slain are not targateble.
Icecrown Icecrown: The Final Goal
Into The Wild Green Yonder: Mounted on the protodrake but can't rescue Captured Crusader Rescuer when clicking on the "Grab Captured Crusader" After further testing I could just hoover above the rescue spot and spam the drop off button and it counted without having to leave the area.
The Last Line Of Defence: Can spam Reckoning bomb without charging it first.
Before the Gate of Horror: Throwing Volatile Acid doesn't count towards quest after killing Skeletal Reaver bones dissolved.
Baron Sliver: Doesn't have the followup quest I Have an Idea, But First....
Baron Sliver doesn't give the followup quest The Duke. after completing The Shadowvault.
Revenge for the Vargul: When you start the event Volgur can not be attacked.
Army of the Damned: When using the rise ghoul as Arthas it doesn't count towards the quests.
Parting Gifts: When you click the Eye of Dominion and get to be an Eidolon Watcher, it doesn't complete in the log.
An Undead's Best Friend: When feeding the plague hounds with the skill from the Eidolon Watcher it doesn't count up (the do become friendly).
From Whence They Came: When using the skill on the Banished Scourge Crystals with the Eidolon Watcher, it doesn't count up (they do dissapear).
Honor is for the Weak: When attacking Restless Lookouts assassinated They can't be killed when you are an Eidolon Watcher. Can be killed without.
New Recruit: When subjugate a Lithe Stalker It doesn't follow you nor can you deliver it to Vereth the Cunning.
King of the Mountain: Can't be completed since the jumps don't work.
I want to thank all the GM's that helped me mapping out the horde story lines of Northrend.
Edit: Things I found later on:
Argent Tournament Grounds
Lance racks don't work to get Argent Lance. You can grab one from inside the instance Trial of the Champion.
The daily's to complete Up To The Challenge: The Aspirant's Seal for the daily quests given by Sunreaver members inside the southeastern tent don't have these. Daily: Training in the Field Daily: Learning the Reins 1 of these daily: The Edge of Winter, A Worthy Weapon, or A Blade Fit for a Champion
The Seer's Crystal: Doesn't show up after completing The Black Knight of Silverpine?
None of the ToC daily's are available but 2 (should be around 8-10) becease you can't complete Up To The Challenge