Continuity mistake: After Wesker flees Arcadia in the Umbrella chopper, though he himself has the ability to heal extremely quickly, his clothes no longer have bullet holes in them.
Continuity mistake: Bennett stabs Alice in her lower arm, from the top to bottom, probably between the bones. But in the revolving shot which reveals Wesker, the knife is suddenly facing side to side, meaning the knife would be going over the bones.
Continuity mistake: After the Tower Swing, Alice lands where she started out: in front of the garage with the UPV. Note the sign with the gun on it. But the door right next to it is closed. Behind that door is the UPV. Since everybody was in somewhat of a rush, it doesn't make sense that anyone should have closed it.
Continuity mistake: Alice is in the shower and draws her gun from the holster on the pole. She takes a couple of steps forwards, camera cuts, and she's suddenly much further forwards.
Continuity mistake: In Extinction, we see Kmart be handed the Alaska book and say "You're not coming?" to which Alice replies "Take care of the others." In the flashback seen here however, Alice replies "Take care of the others, Kmart".
Continuity mistake: In the after titles sequence, when Jill is addressing the group in the plane, she is walking with her hands on her back. When she turns around, heading towards the tail, in the long shot her hands are on her hips.
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.
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.
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.