Other mistake: Pretty much everyone in the film, especially Alice, seems to be able to fire their weapons without reloading at all.
Other mistake: Wesker's chamber on the Arcadia has only one entrance, a big blast door which Alice walks through. Yet Chris and Claire manage to appear behind Wesker without the blast door ever being opened. (01:18:00)
Other mistake: At the end of the fight with the Axeman, Alice points a shotgun towards him, while both she and Claire are sitting on their knees (as is seen in the overhead shot with the axe in the wall). But the shotgun is clearly pointed downwards. Alice is 5'9'', while the Axeman is at least 9 ft. tall. If she wants to blow his head off, she should have been pointing it more up. (01:07:40)
Other mistake: When we see a shot of the plane flying away from under the camera through the mountains, the 2:40 crop (letterbox) is drastically warped in the upper right half of the image. Spotted on the Australian Blu-Ray release. The DVD copy does not have this error. (00:19:20)
Other mistake: During the fight with the Axeman, we get a few shots of him breaking the shower columns. In the overhead shot of Claire, the columns in front of her and way out of reach of the Axeman are already broken, before the flip. (01:03:00)
Other mistake: Throughout Claire and Chris' gun fight with Weskers, not a single shell casing is dropping to the floor and despite every single bullet missing, no marks appear in the walls. (01:20:00)
Answer: Based on the sounds to go with the scene, I'd say it is zombies taking the guards out. However, considering following events it is more likely that Alice and her friends have something to do with it.