When Wallace is being dressed by the machine in the morning, it puts his sleeves on first, then his shirt and cardigan combination. When Gromit is sitting in the seat later, the machine puts on the shirt and cardigan first and the sleeves afterwards.
During the train scene, Gromit is dangling from a lamp on the ceiling. Then Feathers McGraw shoots the lamp, Gromit falls onto the train, and the lamp is on his head. But as earlier seen, there is a light bulb in the lamp, so shouldn't we have seen and heard breaking glass?
When Gromit is in the Techno-Trousers and painting the ceiling of the spare room (upside down), Wallace backs out into the upstairs hallway and bumps into Feathers. Feathers is not there until Wallace bumps into where he is supposed to be standing.
When looking at the calendar, Gromit suddenly has a watch on his right arm. It is not seen before or afterwards.
When the penguin uses the remote to get Wallace out of bed, the sheets are all crumpled up, but in the next shot they're neatly spread over the bed again.
During the train chase, Feathers McGraw fired his revolver 7 times without reloading. Most revolvers only carry 6 rounds.
During the train chase Gromit and Wallace cross McGraw's way Gromit puts a segment over the existing track. It's clear when the carriages between Gromit and Wallace pass that the new track is on top of the old one rather than a cross-track piece. After Wallace snatches the locomotive, McGraw left on a little platform on 4 wheels goes smoothly over the new crossing rather than "tripping" over the crossing rails on top of his track. Even after McGraw makes a turn and reveals the crossing behind for 2 frames you can see the new rails are still lying on top of his track.
When the robot claw on the end of the long metal rope emerges from the motorcycle helmet on Wallace's head, it is clear that it is far too large and there is far too much metal rope to fit inside the helmet together with his head.