Other mistake: In the second scene, where we see the colonel, he is looking through a door to another room. After the door closes, we see that he was looking down, into the room below. But, as we saw in the previous shot, his tie was not dangling downwards as it should have been. It wasn't a Gravity Shift, as he never entered that Cube that the camera was in.
Continuity mistake: Just after Jerry writes the number 4 on the room where he meets Kate and Sasha, they cut to a far shot as he and Kate converse. The spot where he wrote is visible and the marking is gone.
Visible crew/equipment: Just after Mrs. Paley joins the others, the door closes and a boom mic can be seen in the reflection of the door, lowering down a bit.
Continuity mistake: When we first see the colonel, he grabs the suitcase to examine it. In the far shot, you can see that the handcuffs are on the far side of the handle, near his body. The next shot is a closeup of the suitcase, and the handcuffs are now on the opposite side of the handle, away from his body.
Continuity mistake: When Kate turns to see all the numbers appear on the silver frame around the portal, although they are meant to be in the same position and handwriting as when they were drawn, much of the writing is not. (01:17:25)
Continuity mistake: When Jerry scratches a '5' with his watch onto the wall, in a wide shot he starts to scratch the 5, then in the closeup of him scratching it onto the wall, much more of the 5 has been completed between shots. (00:17:35)
Revealing mistake: As Sasha stands up, saying she feels something is wrong, to Kate (in the Razorsphere room), you can see smudges and scratches, revealing a protective glass screen between her and the camera. (00:51:30)
Answer: They sent the agent in to retrieve some sensitive information from the blind girl. The girl hid inside the hypercube as she knew they wouldn't come after her and by the time they figured out where she was it was too late to stop her and so they sent the agent in. They shot their own agent as the information she has is that sensitive that they can't let anyone know anything about it (even the fact that it exists).
Sanguis