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.
In "Brazzle Dazzle Day", when Nora, Pete, and Lampie 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.
During the song "Brazzle Dazzle Day" when Lampie, Pete, and Nora start cleaning the top level of the lighthouse, there's a couple of inconsistencies with the glass door opening and closing as the shots change.
When Pete falls asleep in a hollow log after escaping the Gogans, he is deep in the middle of a dark, murky swamp. But when he wakes up the next day, he is now out in the middle of an open field with apple trees.
Every time someone enters Elliot's cave, we 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.
During "Every Little Piece", Doc Terminus sings "Crowns!", then Hoagy sings "Sous!" The subtitles say Hoagy's line as "shoes". This is obviously incorrect, especially since they are singing about money and sous is an old French coin or a small amount of money.
When Pete is riding the invisible Elliot in the opening scenes through the forest, the wires holding him up are visible.
When Doc Terminus and Hoagy have crashed into the net, the wires holding them up are visible.
While Pete is feeding Elliott apples, one of the apples is seen falling back into frame.
When Hoagy (in disguise) clutches a dollar bill during "Passamashloddy", it is of a mid-20th-century design.
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".
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 "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.
Reflection in glass used to crush the Mayor's cigar.
Passamaquoddy is in Maine, but the sun sets over the ocean, revealing the California filming location. (See Trivia.)
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.