When the evil Ritual Master calls for the crystal bats to fly away to watch Jen and Kira you can see thin white strings as the bats fly from the castle ceiling.
The Gelfling puppets have three fingers and one thumb on each hand. When Kira and Jen make their way into the castle via a mouth-like entrance, Kira's right hand has five fingers in the long shot (actors, not puppets, were used for long shots of the Gelflings).
When Jen and Kira are climbing into the Castle via the water duct, Kira bumps her head on the tooth of the water-spouting gargoyle.
When Aughra squats down and tells Jen "There is much to be learned and you have no time." As she says that there is a piece of hair in her mouth, as she says the line it falls out, but when they cut back to her the hair is back in her mouth.
In the commentary track, Brian Froud points out that the Podling drummer has gaffer's tape wrapped around his neck.