Please note that this list includes breadcrumb quests, any breadcrumbs on this list are actually broken, I know most breadcrumbs become unavailable if you do the followup, this isnt the issue with the ones on this list
Alterac Valley:
The Battle of Alterac (7141 & 7142): Prospector Stonehewer/Voggah deathgrip is meant to offer this when korraks revenge isnt active
Hero of the Stormpike/Frostwolf (8271 & 8272): Prospector Stonehewer/Voggah deathgrip is meant to offer this when korraks revenge isnt active
Alterac Valley Graveyards (7081 & 7082): Sergeant Durgen Stormpike/Corporal Teeka Bloodsnarl are meant to offer this when korraks revenge isnt active
Towers and Bunkers (7101 & 7102): Sergeant Durgen Stormpike/Corporal Teeka Bloodsnarl are meant to offer this when korraks revenge isnt active
Capture a Mine (7122): Sergeant Durgen Stormpike are meant to offer this when korraks revenge isnt active
Cooking:
I Know A Guy… (6612) meant to be given by daryl riknussun, (May have been broken when dailies were added to this NPC)
Fishing:
I Got Nothin’ Left! (6609): This is meant to be given by Grimnur Stonebrand, (May have been broken when dailies were added to this NPC)
Elwynn forest:
Deliver Thomas’ Report (39): This quest looks to have been accidentally marked obsolete during the shattering, theres just a gap in the quest chain
Silithus:
Scouring the desert (9419 & 9422) Broken with the release of call of the scarab world event
BC:
Blasted Lands:
Through the dark portal (10119 & 9407): This quest was broken, (probably during the iron horde invasion of WoD pre patch)
Isle of Quel’danas:
Enter, the Deceiver… (11550): General Tiras’alan is meant to offer this quest
Shadowmoon valley:
Entry into the citadel (10754 & 10755): The keymolds to start these are not dropping as intended, gamemasters are able to provide the mold via a ticket but its not realistic for thousands of people 
Nagrand:
Stealing From Thieves (9882): This is the non repeatable initial turnin for the crystals, its unable to be completed if you get your rep with the consortium to high, like the repeatable one
A Head full of ivory (9914): This is the non repeatalbe initial turnin for the horns, Its unable to be completed if you get your rep with the consortium to high, like the repeatable one
Hallows end:
The Headless Horseman (11135 & 11220): aren’t offered by the Costumed orphaned matrons
Call The Headless Horseman (11392): also isnt being offered by the pumpkin shrine
Free At last! (11242 & 11403): arent offered after killing the horseman, Sir thomas shows up as intended but since you cant do the pre req quest, you cant pick it up
Midsummer:
Ahune, The frost lord (11955): Earthen ring elder is meant to offer this
Ahune is Here! (11696): Numa Cloudstrider is meant to offer this
WotLK:
Love is in the air:
Man on the Insite (24792 & 24793): meant to be given by UNKNOWN, isnt being offered by any NPC
Jewelcrafting:
Writ of Merit (14160) item 47246 is meant to be mailed to the player (I think when they reach 25 northrend jewelcrafting)
Ulduar: You can start the non heroic quest chain via the item Archivum data disc but then it is unable to be continued, prospector doren versions from heroic and normal were not merged
The Celestial Planetarium (13607)
Freya’s Sigil (13606)
Hodir’s Sigil (13609)
Thorim’s Sigil (13610)
Mimiron’s Sigil (13611)
Algalon (13614)
Cata:
Capital Cities:
A Personal Summons (28825 & 28790): Cata intro questline starter, got missed in the hero’s call board update
The Troll Incursion (29156): Missed in transition to new hero’s call boards, no longer any crumbs to this questchain
Guardians of Hyjal: Call of the ancients (29390 & 29391): Missed in transition to new hero’s call boards
Pandaria:
Vale of Eternal blossoms:
A Flash of Bronze (33229 & 33230) No longer triggers when entering Vale of eternal blossoms for the first time
The Lorewalkers (31367 & 31368) Isnt being offered by Scrollmaker resshi/lena stonebrush for unknown reason
The Anglers (31369 & 31370) Isnt being offered by Master Angler Karu/Master Angler Marina
The Tillers (31372 & 31374) Isnt being offered by Farmhand Dooka/Tang Ironhoe
The Order of the could serpent (31373 & 31375) isnt being offered by Wei Lakebreeze/instructor windspear
Draenor:
Lunarfall:
Bounty: Twisted Ancient (33111): During the revamp of heros call board, the bouty board was mistakenly replaced too
Capitals:
Numismatics (38345 & 38346) Disabled by devs due to the coins being bugged (and the rest of its questline!)
Blasted Lands:
Iron Horde Invasion (36498 & 36499) Originally on the “What’s new” menu, It never got moved the the adventure guide
Legion:
Artifact:
A Royal Audience (42978 & 42985) The items that start these quests are no longer being awarded with the pvp honor level artifact weapon appearences
Suramar:
Fighting on all fronts (45317): Broken by some unknown cause
Class halls:
An urgent warning (IDs more than is helpful to list!) There seems to be some phasing issue causing the quest givers to not show up in the class halls, Also rendering the followups broken
BFA:
A mission of unity (53063): Becomes unavailable (I think if your rep level is to high?)
Shadowlands
Maldraxxus:
Sure bet (59882): Au’narim doesnt offer this after you do the pre req
Edit:
Adding more to this list
Threads of fate is completely non functioning in party sync, Attempting causes you to skip 62704 (The threads of fate) due to it phasing not being shared with that quest, 2 people in party sync, only 1 can see the quest giver, you can then activate threads of fate, (text box confirmation and all) upon confirmation nothing happens until you exit party sync, then Re-introductions appears, after accepting and then turning in re-introductions, Nothing happens at all, party sync or no (62000) Choosing your purpose will not show up, I think this because (57878) Choosing your purpose is excluded from replay, and is mutually exclusive with (62000), making continuing threads of fate impossible
possible solution: make (57878) replayable, should be an easy fix