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 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.
During his search for Aughra, Jen dislodges a handful of small rocks that tumble towards the camera (21:40). During this shot, the top of Jim Henson's head briefly pops up twice, visible just above the rock that Jen is walking behind.
At 1:20:01 when the Garthim are being summoned, the Garthim on the top tier can be seen knocking over the first Podling accidentally, indicating that they were placed to stand there for the scene but had no puppeteer assistance.
During the tussle in the Garthim den at 1:13:50, one of the soldiers grabs the Gelfling and hurls him across the room. As Jen lands, he briefly upsets the floor and reveals it to be a soft pad covered in black cloth and dressed with a thin layer of gravel.
The Gelflings never completely blink-their eyelids only partially go down over their eyes. At least once, when approaching Aughra's house, Jen walks right into hanging vines without blinking. Though this is an alien world, most animals that have evolved eyelids have done so to protect the eye, and therefore would have a reaction to shut their eyes if something comes near to the eye.
In the commentary track, Brian Froud points out that the Podling drummer has gaffer's tape wrapped around his neck.
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.
One of the pod people is a drummer. During a closeup, bright blue is visible at the neck, in stark contrast to the dark colors of the puppet's clothing. It is possibly the wrist of a blue shirt worn by the puppeteer.
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.