Vampire Bats and Scaredy Cats - S2-E2
Continuity mistake: When Lisa's uncle shows her her grand-father's picture, it changes from one shot to another.
Hang in There, Scooby-Doo - S2-E3
Continuity mistake: In the cavern, Scooby and Shaggy dig holes in the ground. The rest of the group notice a truck driven by the Pterodactyl going toward them. Discs and cassettes fall from it. The shot later, the stones behind them have disappeared and the pile of discs have a different shape.
Continuity mistake: In the episode of Scooby movies where they meet the Three Stooges, Fred says that Velma is missing and they need to find her. When they go off to look for her they pass a window. Fred first, Daphne, then Velma (despite her being the one missing!), Shaggy, then Scooby.
Hang in There, Scooby-Doo - S2-E3
Continuity mistake: The pile of bootleg records suddenly gets bigger after Velma's shown holding some of them.
The Harum-Scarum Sanitarium - S1-E11
Continuity mistake: Shaggy goes back and forth from being in the front seat to the back seat of the Mystery Machine as the episode starts.
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 Ghost of The Bad Humor Man - S1-E4
Continuity mistake: The back doors of the armored truck that the phantoms are trapped in go from being open to closed to open again.
The Creepy Heap from the Deep - S2-E8
Continuity mistake: Captain Clement's hair and beard briefly go back to his natural grey when he's still in his zombie makeup during the submarine chase.
The Chiller Diller Movie Theater - S2-E4
Continuity mistake: Scooby Dum's collar goes from its usual red to yellow briefly in one shot on the train.
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.
The Harum-Scarum Sanitarium - S1-E11
Continuity mistake: Fred and Velma get chased by one of the dogs into the room where Shaggy and Scooby are. Daphne wasn't with either pair, yet she's suddenly there once Fred closes the door.