When Daphne is riding a horse on the train, the Phantom separates the coach he's standing on and the next one. He remains on the same coach when turning to Shaggy, but when the shot returns to behind him, there's an extra coach along the train where Fred, Velma, and Scooby climb up onto.
The mechanical hand of the gorilla who grabbed the Faceless Phantom shifts left, right and left between scenes.
Velma wouldn't be allowed to wear glasses while filming as a stunt double for a character who doesn't wear them. If it was too dangerous for her to fall off the building without being able to see well, then someone else should've played the part. It also would be highly unlikely to not have them fall off during the descent and chase.
Closed captioning calls Rip, "Rick," even when the former was clearly written in the scrapbook.