When Thumbelina finds the wounded Jacquimo, the thorn piercing his wing clearly entered from behind, yet when she pulls it out later, it has gone through from the front.
During the "Marry the Mole" sequence, the makeshift dress Mrs. Fieldmouse is wearing loses its tail end for a few moments.
When Prince Cornelius flies past Thumbelina's bedroom window for the first time on his bumble bee, he's seen wearing a knight's helmet that he wears on and off throughout the film. However, when he hears Thumbelina singing and comes back into the shot his helmet has disappeared entirely.
Thumbelina and others throughout the film refer to the singing family as toads. However, toads do not swim and the basic character design of the family is definitely that of frogs, not toads.
When the Toad Brothers sing the last chorus of On the Road, their lips don't move.
After Thumbelina agrees to Prince Cornelius' proposal she magically receives wings. During this part she is speaking about her wings but her mouth does not match the words.
Around half the movie would have been avoidable if Jaquimo had carried Thumbelina on his back to her home when he first met her, rather than after she escaped her wedding to the mole.
Mrs. Fieldmouse refers to the mole as "the richest rodent for miles around."
Moles are not rodents.