(at around 1h 1 min) After the demonstration of "the slap of no return", there is a long shot showing the prisoners and the 'demo station'. The demo station still has a complete uncut rope even though it was cut to drop the slap.
(at around 6 mins) As pointed out by the producers in audio commentary, when Dad Asparagus is coming through the revolving door to the Seafood restaurant, his head goes through the ceiling as he "walks" in.
As pointed out by Mr. Lunt in the commentary, one scene has Laura's mouth grow to an unnatural size.
(at around 20 mins) During Jonah's song rejecting the Lord's call to Nineveh, Jonah is on a giant map of Israel. The city of Joppa is shown well inland. Joppa is a port town on the Mediterranean, and is shown as such in the next scene in the movie.
(at around 17 mins) When Jonah is in the process of receiving the oracle for Nineveh, he asks, "Where would you like me to go? Jericho? Damascus?" just before it is revealed that he is unwilling to go to non-Israelite towns. In the song that follows, he again states his willingness to bring a message to Damascus. Damascus was never an Israelite-controlled city, but was rather the capital of Aram (now Syria), making it just as unappealing as Ninevah (the capital of Assyria).
(at around 1h 2 mins) King Twistomer refers to the whale as "The Great Fish" even though whales are actually mammals.