During the "Money" song, there is a close up on Doc Terminus and Hoagy. When Doc sings the phrase "Can't you hear that jingle-jangle sound", you can see Hoagy start to sing along with him and then catch himself and stop, since the audio only has Doc singing the line.
When Pete is riding the invisible Elliot in the opening scenes through the forest, the wires holding him up are visible.
During the song "Every Little Piece", Doc Terminus sings "Crowns!", then Hoagy sings "Sous!" The subtitles say Hoagy's line as "shoes". This is obviously incorrect, singing they are singing about money and sous is an old French coin or a small amount of money.
When Doc's men are trying to capture Elliott in the warehouse and the Gogans are trying to capture Pete, Willie and Grover alternate from assisting in the capture of Pete to assisting in the capture of Elliot in between shots throughout the scene.
When Hoagy (in disguise) clutches a dollar bill during the song "Passamaquoddy" it is of a mid-20th-century design.
In the Razzle Dazzle Day number, when Nora, Pete, and Lampy are ascending the lighthouse, Nora and Pete have paint all over their arms and hands. When they reach the top and begin to wipe the glass, they are clean.
Reflection in glass used to crush the Mayor's cigar.
When Doc Terminus and Hoagy have crashed into the net, the wires holding them up are visible.
In the song "There's Room for Everyone", Nora sings the lyric, "A dragon is just one more stranger in search of a friend," but she mouths the word "person" for "stranger".
During the song "Brazzle Dazzle Day" when Lampie, Pete, and Nora start cleaning the top level of the lighthouse, there's a couple inconsistencies with the glass door being opened and closed as the shots change.
Every time someone enters Elliot's cave, you see the same scene of waves in the background with the same color sky. Even when Nora looks out from the lighthouse it looks black, but then from Elliot's cave which is just down the beach, it's light blue.
In the cave scene, the tic-tac-toe design moves from Elliot's chest down to his belly when Pete draws a line. Then it jumps back to his chest when Pete leaves with Nora.
During the storm, a huge wave breaks the lighthouse glass and puts out the wick. In the final scene at the lighthouse which takes place the next day (when they wave goodbye to Elliott), the glass is entirely intact.
Passamaquoddy is in Maine, but the sun sets over the ocean, revealing the California filming location. (See trivia.)
When the "Bill of Sale" song is being sung, near the end of it when they are all flying in the air and all saying "We've got a bill of sale right here," Merle is singing when Willie is up in the air and vice versa.
When Nora and Pete are singing 'It's Not Easy' and Nora sings the line 'Life is lollipops and raindrops', she mimes the word 'rainbows' instead of 'raindrops'.
When the Gogans arrive in Passamaquoddy to get Pete back, Willie is not present. When the song, "Bill of Sale" begins he's there.