Continuity mistake: When Shaggy and Scooby find the "Faux Ghost" ticket, they pick it up and examine it carefully. The Black Knight came and they ran away, dropping the ticket and never picking it up. But when they are back in the Mystery, Inc. headquarters, they have the ticket.
Revealing mistake: When Velma is running from the two one eyed skeletons she goes into what looks like a warehouse and the floor is all wet and in some places there are puddles. When the skeletons come they step into a puddle but the water doesn't even splash or ripple.
Visible crew/equipment: When the gang break into the house at the beginning we see Shaggy playing with an old record player. It suddenly turns on with a bang, and if you look quickly when the camera returns to the Shaggy, you can see a hand on the left side of the screen (with what looks like the remote to turn the record player on) quickly pull out of view off screen.
Continuity mistake: When Daphne uses the jumper cables on the 10,000 Volt ghost, she and Fred get blasted away. When they get up, both are covered with soot and ash, however in the next scene when they meet up with Shaggy and Scooby, they are perfectly clean.
Continuity mistake: When Daphne and Fred attach the jumper cable to the Black Night Ghost and the 10,000 Volt Ghost, they run away as the monsters explode. We see different shots of the monsters exploding and then we see Daphne and Fred in the corner running away a second time. It's the same shot as before.
Plot hole: In the scene where Heather and Daphne are talking outside the museum, supposedly Ned changes into the costume of the evil masked figure and goes on the roof of the museum. However, when Heather says, "Scoop of the night, gone." you can see Ned in the background pointing the camera to the roof of the museum. You also hear Heather say, "Ned, get your camera and follow me." as she is walking off. Ned can't have got down from the roof and out of the outfit that quick.
Factual error: At one point in the film there is footage on the news of Mystery Inc's embarrassing attempt to stop the ghouls from stealing costumes. In particular, it focuses on Shaggy and Scooby being dragged across the table, etc. But look at the angle it's taken from: no one could have taken that.
Other mistake: When the gang are watching the news report in their van, Heather Jasper-Howe shows the clip of Fred saying "I think Coolsville sucks" - problem is that there was not enough time for the crew to edit Fred's short interview and be able to transmit it that quick.
Continuity mistake: When Scooby puts down all the stuff he found in Wickle's' manor and Shaggy says those are just stuff Scooby wants, the toilet brush is on the left for Shaggy and it's standing up. When Scooby picks it up, he picks it up from Shaggy's left side, while it is slightly lying down.
Revealing mistake: Just after the pterodactyl ghost has been "tied up", it flies off. When Shaggy and Scooby are looking at the ropes, Fred and Daphne duck at the same time. Obviously it was meant to look like they are ducking when the pterodactyl's wings flap, but the pterodactyl has already flown off.
Continuity mistake: After Velma suspects Patrick the Curator of being the evil masked figure, she tripped on the catwalk. She was holding onto one single grate then in the next shot she was holding two, then in the next shot, she is holding one again.
Continuity mistake: In the fight scene at the library, you can see Daphne's boots change from stilettos to boots with a smaller heel and back to stilettos again.
Revealing mistake: When Fred rushes in to fight the Black Knight Ghost in Mr. Wickles' castle, he is hit in the face several times with the back of his shield. As he falls, you can see the pad on the back of the shield to protect his face. (It is not noticeable when he first runs in.)
Continuity mistake: When the gang gets back to the Mystery Inc. Headquarters after searching for clues at Old Man Wickle's, Daphne's boot heels are higher.
Continuity mistake: When Daphne is fighting the Black Knight at Old Man Wickles' place, notice that the stunt double's hair is longer and straighter than Sarah Michelle Gellar's.