When Haskell is activated, they turn on "pain suppression" as one of his attributes. If so, he wouldn't have felt anything when Rains kicked him in the groin.
When Meyerhold throws the boot into the ice trap room, he does not hold on to the shoelace, and the boot is shown flying through the air with no strings attached. When it is frozen and shatters on the floor, the next shot is of Meyerhold pulling up a shoelace with a block of ice attached to it.
When Rains first meets Haskell she spits on him. It is obvious that when she spits the spit goes almost directly onto the floor yet Haskell wipes it off his upper cheek, which is several inches above Rains' mouth to begin with.
When Wynn looks at Rains' file, the drawer her file is in is slightly open before he finds it. The shot cuts to Dodd reading the paper, then back to Wynn, and her drawer is shut.
In the first 3 minutes of the movie, Ryjkin is sprayed with water from head to toe, soaking his clothing. In the very next scene, his clothing is bone dry, yet his skin is still dropping water.
The file cabinets in the observation room are marked with name ranges; one drawer is listed as "Rabinovich - Rabe", which is not in alphabetical order.
The character makes a chess move P-K2 (Pawn to King 2).
All pawns start on the second square, and they can't move sideways or backwards, so that is only possible if the Pawn started on K1. Which is not possible.
Dodd and Wynn are instructed to record the REM Sleeper in room 172409. During the REM Sleep recording, Rains sees herself kidnapped, and then she sees the kidnapper watching Rains. Neither of which is possible from any point of view. You would only be looking at your kidnappers.
When Rains pushes Wynn into one of the walls inside the cube, it wobbles.
When Wynn says he can help the team avoid the traps of the cube, Rains pushes him back into the wall. On impact, you can see the supposedly metal wall behind him move.
When Rain first wakes up, and is looking for her daughter, the shadow of a camera can be seen on her clothes.
When Haskell falls feet-first from one cube to the one below it, Wynn says, "There's no way he could have survived that," and he turns out to be correct. However, earlier in the film, Meyerhold makes the same fall head-first, and is able to stand and operate without apparent injury (except for a giant wound on the side of his face).
Right before he asks Dodd about the "third exit", Winn shows him how to win the chess game that he is studying. First of all, the position on the board is totally different than the one printed on the paper Dodd gives him. What's more, any chess player would agree that his 'solution' is ridiculous: black's last move (rook to e8) simply allows white to deliver a rather obvious mate in g7 when there were several ways to avoid it. It's impossible that an avid chess player like Dodd would not notice such a bold mistake, let alone qualify white's play as incredibly brilliant.
During the chess game in the beginning after Dodd, who is playing White, moves K-Kb8, Wynn then puts him in check by moving Rook takes Quees-check (RxQ+), Dodd's next proceeding move is Bishop to Queen Knight 7 (B-qN7) which would not move his King out of check from the Black Rook on the 8th file which would be required.
When the characters discover the coordinates, they discuss using them to find the edge. However, they are in room C, I, A. Since there is an A in the coordinates, they should have realized that they are already at the edge. (That may have been an incorrect conclusion, but it's the obvious logical conclusion based on their assumptions.)
At the start, Dodd's 1st chess move is Pawn to King 2 (p-K2), while it is actually Pawn to King Bishop 7 (p-kB7).