The miniguns that Jill and Chris use to fight the boss creature on the Queen Zenobia appear from nowhere, not being in the helicopter before.
Jill fires a missile launcher from inside a helicopter. Man-portable missile launchers have significant backblast to avoid recoil, which would kill or incapacitate anyone within the helicopter.
A 3-round burst should not be possible with a revolver.
The Beretta 92FS is capable of holding 15 rounds within its magazine. In-game, it holds only 10 without modification, and this is an example among many of incorrect ammunition limits.
None of the team members ever wear any sort of protection despite sticking their hands into unknown biological material.
There is somehow still air on the Queen Dido, even though the rust within it should have removed all the oxygen.
The Queen Zenobia's communications system requires the main power to function. Considering that communications equipment would be vital in an emergency, it should be able to use auxiliary power as well.
In spite of dealing with an unknown virus, no measures are taken to properly contain the virus.
When Parker calls Jill saying that he has found Chris, Jill never asks how Chris is doing.
Chris states that the satellite laser fried all electronics, but the radios somehow work.
Chris does not express concern over Jill having been immersed in virus-contaminated water. He wasn't told that she had received the vaccine, either.
Grinder states that attacking beasts are just wolves, when they are really B.O.W.'s.