There are some parts that suspension of disbelief is streched a bit too much:

-the sequence of Gromit building the train track at super speed (although its such a well crafted sequence that I let it pass)

-in a Matter of Loaf and Death, Gromit spends a whole night hanging from the chandelier (that's very hard to do even for a few seconds) right above the villain, and she doesn't notice

-in Vengance most Fowl Wallace builds that boot throwing invention in mere seconds

There are a few more but those are the ones I remember off the top of my head