Picked up all 3 codex pages, but the scripting decided to not register 1 page; however if registers to the point that the quest lets me do the final objective but without letting the quest complete. Have had this happen a few times now.
I had this happen to me when I picked up a page while in a dialogue with the guy who opens the sphere with the page in it.
I think it's consistent game behaviour (not sure if it's new or I never encountered it before), that if you pick up a quest objective item while in another dialogue, the game will let you pick it up but won't register the objective as having completed, so the quest breaks (same thing at end of TOEE pt1 very recently too where there's the journal to read and a thing to pick up next to it).
This needs a fix to either register objectives as complete properly or at least stop you picking things up if they won't register.