Your "plot holes":
"all the xenos killed before they got there"
--They killed ONE: the Big Chap. And his blood is what put that giant hole in the floor. The others in the hive came AFTER that.
"...she proceeds to shoot 400= rounds and it doesn't breech the hull"
--95% of them went directly into xenos courtesy of the aim assist. The ONLY ones i could be with you on were the few she fired to avoid the acid, but how far are they inside the ship at this point? Unless you're quite close to an outer bulkhead it's not going to go halfway through the entire station before metal slows the round down and it stops.
"Rook/Muthr's A.I...."
--It was "uploaded" via the disk taken from Rook. That gave Andy upgraded credentials, and also repaired his motor functions, but his core memory remained the same (he literally said so in the dialogue). they needed to ressurect rook to find out how to remove the facehugger safely from Kaye (they literally said THAT in the dialogue, too)
Sometimes i wonder if it occurs to people that what they perceive as "plot holes" might instead be a gap in their understanding caused by not paying attention?
Probably not.