When Jimmy dresses up as the angel, he wears white gloves, then at 1:29:20 he isn't wearing white gloves. Afterwards he then again wears white gloves.
A shot of Living Island at 11:15 (an artist's rendering) does not match a later shot of a real island for Living Island at 46:51.
At 11:10, as wet, monstrous hands grope Jimmy's pectorals, Jimmy's hat blows off for the second time. Scene cuts to a wide-shot camera. Not only is Jimmy's hat back on his head, the monstrous hands are nowhere to be seen, and Jimmy, though heard calling frantically for help, sits calmly in the boat.
When Jimmy and the gang dress as angels before entering Witchiepoo's castle, Pufnstuf appears to be seen dressed as an angel with them, causing confusion because they had not yet saved him from the witch. This is actually Pufnstuf's sister, Shirley.
Wrong way wind reveals that the boat is being towed when it takes Jimmy to Living Island. It moves forward against the wind, which wraps the sails onto the mast and rigging, both before and after Witchiepoo transforms it to evil.
During the Living Island number, the wires that make the frog jump are visible.
When the camera zooms in as Witchiepoo falls to Earth with her umbrella, the wires suspending her and Orson can be easily seen.
At 50:48, when Witchiepoo climbs up out of her castle moat, the rock surface moves under her weight, revealing that it's a soft material, perhaps foam rubber. The same reveal happens at 52:24 when Stupid Bat collides with the "stone" archway of the castle.
In the song "Living Island," Jimmy's mouth has a losing struggle syncing up with the double-recorded lyrics due to the frenetic choreography.
When Witchiepoo kidnaps Freddie the flute, the wire that makes the flute move and talk is visible when Witchiepoo is holding it while steering her flying broom.