Plot hole: How does Horatio (a Lilliputian) get to Glumdaclitch's dollhouse, which is on the second floor of the house? Jack Black is twelve time smaller than the Brobdingnagian, and the Lilliputians are twelve times smaller than him. How did he get up the stairs? Getting to the second story of the dollhouse would be challenging enough.
Deliberate mistake: When Gulliver is first placed in the dungeon, he is attacked by a tiny seagull, however comparing the size of the bird with Gulliver's foot, it appears to be about the size of a fully-grown Lilliputian. This was obviously done deliberately as a correctly-sized seagull would be far too small for the joke to be effective.