The Creepy Case of Old Iron Face - S3-E7
Continuity mistake: The dock at Skull Island is deserted. A shot later, the magnetic crane suddenly appears.
The Creepy Creature of Vulture's Claw - S3-E10
Other mistake: The whole time Professor Greer's the Mantis he's around seven feet tall. When he's unmasked he's suddenly his own size again.
The Creepy Creature of Vulture's Claw - S3-E10
Deliberate mistake: Professor Greer's fleeing from the room one moment, then suddenly he's behind the gang dressed up as the Mantis.
The Creepy Creature of Vulture's Claw - S3-E10
Plot hole: It's not explained how Professor Greer, a man of medium height, say five feet seven inches tall, could make himself look like he's seven feet. Maybe stilts but those would surely protrude out.
Scooby's Chinese Fortune Kooky Caper - S3-E12
Continuity mistake: When Shaggy and Scooby start changing the Mystery Machine's back right tire, it's flat. When the Moon Monster shows up it's fixed, and they've just started jacking it up.