Sometimes the completion of a Timewalking Dungeon doesn’t count for the Great Vault.
It happened to me consistently in Black Rook Hold (can’t remember a run that counted there). Additionally Darkheart Thicket didn’t count but that was probably due to Dresaron being skipped.
I have the same problem this week! I completed 8 dungeons and I have only 6/8. After my 7th it was already stuck at 6/8 and I did another one to check, still at 6/8 
(edit to add: I sent a ticket to report it and I still don’t have an answer)
I completed the weekly quest to do 5 Legion timewalking dungeons, I have the reward and everything. But my vault only shows 3 dungeons completed.
I don’t need 593 gear. I just want that extra slot so I get more tokens to buy crests. I’m a filthy casual so that’s my main source for runed crests.
my brother found this when I was wondering the same thing Timewalking dungeon not filling up Great Vault slot (reddit thread on wownoob subreddit)
specifically this comment/quote for those who don’t want to go on reddit:
If you skip a boss in TMW it doesnt count for the vault, you must kill all the requiered bosses (not the optionals)
could fit, because whenever I landed in legion’s nightmare dungeon, people often if not always, skipped the dragon boss there.