Scooby-Doo Meets The Boo Brothers is one of the few Scooby-Doo movies which has slight controversy regarding the mystery's conclusion. Most prominently, the Skull Ghost clearly has differences in its appearance each time it appears. In the first appearance, the Skull Ghost is all bones and has glowing red eyes. In other appearances, the Skull Ghost appears to be a man in a black suit and has no red eyes. Some believe this means that the ghost was real in the first appearance, while others agree with Shaggy, Scooby, and Scrappy's conclusion that the Skull Ghost was the Sheriff's brother each time.
In addition, it is left very unclear whether Uncle Beauregard was real throughout the movie and in which appearances he was real, if any. Though it's a pretty common conception that the ghost's final appearance after the Sheriff was taken to jail was the real ghost of Uncle Beauregard, the Sheriff never actually admits to dressing up as Beauregard's ghost, so therefore it is simply speculation that he dressed up as that ghost as well. Conversely, it should be noted that in one of the appearances, the ghost had to use a secret passage to make it through the wall, which is not something a real ghost would necessarily need to do.
Lastly, we are not technically sure which category the Ghost in the Attic or the glowing-eyed wolf (which the gang encountered as they first arrived at the mansion along with the Headless Horseman) falls into. The Ghost in the Attic, while likely Farquard, was never confirmed officially in the movie. The wolf is never seen or talked about after the initial appearance, so it is completely up to interpretation whether that ghost was real.
I realize this is a rather long fun fact, but I admittedly find this "controversy" (or whatever you want to call it) quite intriguing. If you have a stance on which ghosts were real and which ones were fake, what do you believe and why?