In the beginning of Jill's scenario, Barry gives Jill a lock pick, claiming her to be an expert in using one. However, it is described in the game manual that Barry is an ex-SWAT team member, who are trained to use lock picks in various properties.
Towards the end of the game (if played correctly), the warning announcement on the PA says: "Unlock all routes for evacuation," but because of the triggering system being activated the entrance elevator is stalled. Also there are a few doors that are still locked under the triggering system.
In the underground Arklay Lab, there are a few rooms where there's a red light that would light up under an emergency. Once the triggering system is activated (an emergency situation), those red warning lights never lit up.
In the Jill game-play, when Barry drops a rope for Jill to climb down, after she climbs down, the rope falls and completely disappears. However, there's no hole or trap door in the floor for the rope to disappear. The rope literally went through the floor and the game went on as if it really did go through the floor.
The second time you fight the Yawn Snake, you can see large bullet holes on its head, but when the Yawn Snake slithers away after the first fight, it doesn't leave with the bullet holes you would of left it with after battling it.
The goof item below may give away important plot points.
Towards the end of the game, your playable character reaches the B-4 level where Wesker is waiting for your arrival, but strangely the only elevator entry was out of power. So Wesker shouldn't be able to reach the B-4 level before you did if the power to the elevator was turned off.