Around 24:44, Chino removes his left shoe and throws it through the window testing the force field. As he jumps on the bed to escape, he clearly wears a black sock. In the next scene of him running away, his sock is now white.
Some of the footage of the cops searching for Chino Rivera is later repeated in their search for the creature. In fact footage of the other dead cop found by them is shown twice (so one time before the death is even shown onscreen).
When the Chromomite is feeding at the lake, sometimes his mouth is on the right shoulder, and in other shots his mouth is on the left.
At 14:30, Chino rises slowly to stand beside Dr. Julia Harrison while they listen to the alien voice over the loud speaker. When the camera angle switches to a long shot of the room, Chino no longer stands beside Dr. Julia. In fact, Chino is missing from all of the long shots of the room.
It's never questioned how the Chromomites, who are awkward blobs with clumsy three-fingered claws, could produce the advanced technology needed to facilitate the teleportations.
When Chino trips and falls onto the body of Dr. Richardson, no sooner has he landed the two wardens pull guns on him from mere inches away. There is no way they weren't already close enough to see him run and fall, let alone commit murder by drowning.
The alien goo they are examining in the laboratory is obviously bread dough.