Factual error: In the scene where Alice lands the plane on the roof of the prison the length of the roof is far too short to have landed in that distance at the speed they were traveling. The wings also impact several solid objects during the landing which would have damaged them, if not severed them completely. At the end of the landing the nose smashes through a solid concrete ledge at the end of the run. The propeller is too fragile and should have shattered in an impact that forceful but instead remains completely unscratched. (00:31:00)
Factual error: Alice blows up the wires of the elevator to bring it down as quickly as possible. But all elevators have emergency brakes to prevent precisely that from happening. The chances of them being damaged by rust are also very slim: they are covered in grease. (00:59:35)
Factual error: Alice isn't superhuman in the scene of the Tower Swing. But at the rate she is falling, she would both hit the ground before the cable would be under tension, and even if the prison was high enough, it would probably shatter every bone in her shoulder when it does become tensioned. (01:01:00)
Factual error: Just after Alice jumps from the tower and draws her dual revolvers, the film slows down to bullet time to show her shooting two zombies. If the speed of the bullet is accurate, there's no way she can move so fast as to then run and get out her shotguns. (01:03:40)
Factual error: The blood stream on Wesker's head is wrong. He is leaning over to his right, and the blood coming straight out of the wound is going slightly to the right, and then straight down, so far so good. But at the angle he is lying, the blood should have stopped at his eye, and even if it did jump over his eye socket, it should have been directly below or even more to the right of where the first stream ends.
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.