It's funny. About 5 minutes after I posted no glitches I ran into one.
There's a spot on mothership zeta, fairly far along, where the game progress event wouldn't trigger for some reason.
It's right after the space walk sequence. Your supposed to activate a teleporter to allow your helpers to join you. Well for some reason they wouldn't come through. Luckily I had been saving frequently. Quit game, restarted the console and picked a relatively close save point start from and it triggered.
Glad it was an easy fix.