Looking down on the Neverhood from the asteroid with the pin will show the combined bridge/staircase in "bridge mode", although it was actually in "staircase mode" when the player left.
After Big Robot Bil starts lifting up the gate, it briefly appears closed, and then Bil starts lifting it again.
The clay is visibly scraped off the cannon's platform by the cannon's base as it turns. It is back to normal in the shots thereafter.
Though the Neverhood is supposed to be situated in a dark void, sometimes we can see light reflecting off the black cloth in the background, as well as the shine of the studio lamps.
Klaymen is misspelled as "Klaymeb" in one of Willie's letters. This might or might not be deliberate, since Willie is a pretty dumb character.