When it shows the mansion at one part, as lightning flashes with a clap of thunder, the lights in one window of the place keeps flickering on and off!
When Daphne points out to Velma the loose floorboard, she's speaking with the latter's voice as she continues to tell her to watch where she's walking.
Before the big chase scene, Daphne decides to hide in the closet in her room. The other four go in with her, but then they're all scared out by the ghost who's already inside. The same four run out--WITHOUT Daphne--with the ghost in pursuit.
Shaggy and Scooby are shown running away from the ghost after attempting to get a late night snack. Scooby runs ahead and into the bedroom that he and Shaggy share with Fred, slamming the door on his way in. Before Scooby can make it to the bed, Shaggy pushes the door open and Scooby is crushed between the wall and door. Stopping dead in his tracks, Shaggy turns back to shut the door, then, runs toward the bed.
The scene returns to Scooby, who is now standing in front of an open door -- the same one that Shaggy closed just seconds before.
When Scooby falls down the chimney, his spots are missing.
Phineas's peg leg alternates from left to right leg from scene to scene.
Don Knotts: (After Scooby sniffs a sock whose odor causes him to faint) That's the test that separates the rookies from the pros.
Fred: It's only a......cuckoo clock!
The ghost of Captain Moody appears in Scooby Doo Night of 100 Frights.
Throughout the second run of the series and later reruns, a segment that was absent during the first run was added in. In this episode, it's a scene where the gang is looking for a secret passage that Scooby finds, but he can't get the kids to notice. He gets Shaggy to land in a pile of dust, and sneeze his way to the secret passage that the gang volunteers Scooby to climb. This scene is intact on the DVD release.