I'll add...
What was the Big Chap from the first movie encased in, rock?or did it cocoon itself?
The kids were virtually slaves on the colony planet, yet they had access to a WY freighter that they could come and go in, with no restrictions or air traffic control?
What was the deal with Romulus/Remus? If Romulus was the administration /control side and Remus was the experimentation/breeding center as implied, why were there facehuggers stored in Romulus?
The big hole that had been burned in the floor by acid blood didn't breach the hull somehow? That was a big hole, seems unlikely the acid would have burned itself out, especially given Andy's warning about the pulse rifles.
The freighter just happened to spin out of control right into the cargo bay, with no significant damage or depressurisation of either?
The black goo has Engineer DNA? Why? Wasn't it meant to be a bio-weapon designed by the Engineers, not made out of them?
I dunno, it seems like they spent the whole time on production design then filmed a first draft