Corrected entry: 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.
Corrected entry: In the scene where the gang find the museum broken into for the second time, Velma's hair is straight from when she had her makeover. After that they go to the Mining Factory and her hair is black curled. She could have changed out of her outfit but I doubt she had time to do her hair.
Corrected entry: There is a scene in which a ghost shoots harpoons through the back door of the Mystery Machine. In the next shot, the harpoons are gone but there are no holes in the door of the van.
Corrected entry: When the Black Knight and the 10,000 Volt Ghost are attacking both Fred and Daphne, Daphne pulls some jumper cables out from the Mystery Machine however just before they made it to the junkyard they show several scenes of the van's interior with no jumper cables visible. Those cables were huge and would be rather uncomfortable to be sitting on.