There's A Demon Shark In The Froggy Dark - S1-E9
Deliberate mistake: Unless they're super strong, none of Mystery Inc could've thrown an anchor to the top of a cliff.
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.