Plot hole: Det. Kerry says at the scene of Paul's trap, "He had two hours." There is no way she could have known that. The clock simply said 3:00 and the tape specifically says "you have until 3 o'clock or this room will become your tomb". No way to know that's two hours after the fact. (00:17:30)
Plot hole: The secret CIA base at Kamp Woody was underground. Kids searching for years have combed the camp, but never found it, but when Cody is going down the escalator, you can see bright skylights on the roof. If the sun is able to shine through, that means the skylights aren't hidden, and the kids would be able to find the camp.
Plot hole: Sonny hides among the 1000 robots in the big store room. They are all placed in very straight rows. Sonny would not be able to take over another robot's place in the grid (when he starts running we see a large robot-sized gap) without getting another robot to move. And while Will Smith is running around the rows, he would have noticed if the others moved to make room.
Plot hole: After Noah stabs Lucius, Ivy is brought to see Noah who is locked up in the "quiet room". As they leave, the lock is being placed on the latch to lock Noah in, and soon after the door is rattling, presumably Noah in an attempt to open it. If you look closely, you can see that the rattling occurs because the door lock is locked and not because of the lock on the latch. Quite strange, as we clearly see the lock placed on the latch right after the door is closed. There could not possibly have been time for the door lock to be locked with a key.
Plot hole: When the fat guy throws a boot into the ice-spray room, it freezes and shatters on the ground. You can see the length of the shoelace on the ground as well. The shot cuts to the guy in the shaft, and he pulls up the shoelace to reveal the end encased in ice, while the end is halfway into the ice block. This wouldn't be possible, because the other end of the shoelace had no ice at all, and there's no sign either of it breaking.