Continuity mistake: When Issacs is choking Alice, she's seen to stamp and break the floorboards. Camera changes and the floor has been repaired and Alice's position has changed. (01:20:20)
Visible crew/equipment: When we first see the wet floor in Tokyo, look carefully to see the reflection of the boom arm moving. (01:23:00)
Revealing mistake: Near the end of the movie when they are showing Tokyo and the camera pans down through the street to Umbrella's underground HQ, you can see a rat leaning over the 'edge' of the road as it is going down. (01:23:10)
Revealing mistake: In the scene where the cowboy character is climbing the Eiffel Tower, you can see the shadow behind it only goes a few feet above where he is. Revealing that the tower is not a completed structure as shown in all of the wide shots.
Other mistake: In the end fight scene between Dr. Isaacs and Alice, she bumps into the water cocoon and awakes one of her clones only to have it die a few seconds later. When she goes to cover up the body, the clone can be seen wearing a wedding ring - they don't incubate the bodies wearing jewelry in an embryonic state.
Other mistake: In order to use the vials that have either the T-virus or the anti-virus it has to be loaded into a special gun-like tool, similar to a caulking gun. A plunger is then set, and released with a trigger, again, like a caulking gun. The problem is that when the vials are seen, the caps on either end are solid, with no hint of an opening for the fluid to get out and into the body that it is being administered to.
Chosen answer: The reason that the cloned alices were put through the tests was their attempt to get a "perfect" clone of her. They knew that Alice was the key to taking back the zombie infestation, so they were trying to get the "perfect" clone. The perfect clone would have all of her memories and reactions, so they put the clones through that testing facility. If she made it out alive, then she was the perfect clone. If she didn't, then it was back to the drawing board.
Nick Bylsma