I cant finish while missing 1 or 2 Animus Carriers in Dungeon: Shifting City. I run through the dungeon several times and did reenter the dungeon but cant find it.
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I got this problem too in version 1.0.4.42942.
After searching the empty dungeon for 15 mins unsuccessfully, I left and rejoined the game (thus forcing the dungeon to reset) and it worked on the second try.
I did note that some sites on the internet suggest that the issue could be if enemies are killed before the Animus Collection quest activates, which might be possible but that seems unlikely here because the first animus carrier isn’t until a fair bit into the dungeon after the quest activates.
Still seems to be an issue as of patch 1.1.
Still an issue, and I just encountered it on Xbox.
Aug 30 after patch 1.1.3 - im missing 1 and can’t complete it 
Usually its because you missed a dot of annubus juice. Gotta back over the map & find it. That should resolve this issue forever. Lol