Factual error: When the people of Lilliput find Gulliver's boat, he picks up his cell phone and says he doesn't have any signal but has 11 messages and proceeds to listen to them. If you have no signal at all, you wouldn't be able to check your voice mail.
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.
Revealing mistake: On Gulliver's MacBook when he is plagiarizing , he has the wrong program active at the top (Finder for Macists), when he is typing on the keyboard. He also doesn't have a single word-processing application open, which can be viewed at the bottom.
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.
Deliberate mistake: At the beginning of the end credits, the newspaper article just repeats itself. Plus, it has a weird shift of going from a first person account to a third person review of the original book (including mentioning George I was King of England at the time of the writing of the Travels).