Continuity mistake: Alice stabs Wesker in the head with the handle of the scalpel tilting over to Wesker's left side. In every shot afterwards, it's facing to Wesker's right.
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)
Continuity mistake: Alice ties Claire up to a double engined plane. In the satellite shot, it changes to a single engined plane. (00:25:00)
Continuity mistake: In the overhead shot with the falling glass, Alice's second shotgun is apparently lying under the table, because we can't see it. When Bennett attempts to pick it up, it has moved itself a good foot and a half away from the table. (01:24:00)
Continuity mistake: In the front shot of Alice just when see jumps off of the roof, in the far right corner of the screen, one of the zombies trips and falls down. But in the wide-shot directly afterwards, that zombie is instantly gone.
Revealing mistake: Just after the Tower Swing, Alice shoots with her Smith and Wesson at a load of zombies. But when she fires the last two shots (the ones in slow-motion) pay close attention to the gun in HER right hand. The chamber doesn't start to turn until after she has fired the shot, meaning that the hammer would strike a spent bullet.
Continuity mistake: Right after Alice lands on top of the prison, she makes three skid-marks on the roof: one with each wheel. These are seen best in the shots which show the front of the plane. But in the overhead shots, the skid-marks are gone. This can be best seen in the shot where Luther grabs hold of the tail wing. (00:32:50)
Continuity mistake: When Alice kicks Bennett away, he lands one one of the dead bodies, sliding it back significantly. But in the shot where the dog is splitting its head, you can see the head of the body in the top right corner of the screen. And it definitely is the one Bennett landed, seeing how that was the one next to the shotguns. And in later shots, you can see that all of the bodies are in their original positions. (01:18:00)
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)
Visible crew/equipment: Immediately after the scene of The Executioner beginning his walk to the prison, there is an aerial shot moving toward the prison in which the camera plane's shadow can be seen on the right of the screen. (00:45:20)
Continuity mistake: Right after the Tower swing, Alice draws her shotguns, ready to shoot. In the close up shot of her, the shotgun in her right hand is pointing up. But in the far shot with the two zombies in front of her, it is pointing down instantly. (01:03:55)
Continuity mistake: When Alice is shining her flashlight into the tunnel, in the far shot from the inside of the tunnel, she is leaning on a rock, on her elbows. But in the shot directly afterwards, she is still leaning on the same rock, only now on her hand. (01:01:50)
Continuity mistake: Before the opening fight scene, we can see the guards running towards the entrance past a row of Hummer H2's. But after Alice blows the second group away and takes out those cars, they all of a sudden change to H1's. Also it can't be one from the opposite end, because those have a pick-up truck rear end, and the one lying on its side has a slanted back end. (00:07:15)
Continuity mistake: During the initial fight scene, one of the Alice clones takes cover behind a pillar, which is fully intact. When the shot cuts to show her and the other clone, there are three bullet holes that have mysteriously appeared in the pillar. (00:11:10)
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.