During a 20th anniversary screening of this film, Doug Jones revealed the moths that come out of his mouth at the end are real, not CGI. In a 2018 interview with Bloody Disgusting, makeup and special-effects designer Tony Gardner said that the actor wore a "mouth rig" a latex pocket attached to dentures that blocked off Jones' throat to make the moths come out "There was a small hole in the very back of the pocket so that Doug could cough some air through it ... An animal wrangler would place several moths in the pocket with tweezers, Then the stitches would be glued shut, and we'd run out of frame so that they could get to the shot as fast as possible," Gardner said.

After Winifred dies all of her spells were undone including the spell that transformed Thackeray. It can be assumed that when he transformed his body was killed and it was only his spirit or soul that took the form of a cat. When Winifred dies his soul was released and was allowed to pass on.

During the end credits, the parents finally stop dancing and leave the building, exhausted; Jay and Ernie have been forgotten about and are still dangling in their cages, singing Row Row Row Your Boat, then the camera pans over to the spell book as the eye opens once more.

When shown on UK television in 2005, all instances of Billy losing his head and stumbling around headless were cut (rendering the credit in the cast to 'Headless Billy' meaningless). Thus, the scene when Billy loses his head and Dani steps out of the protective salt circle to retrieve it for him (giving Winnie the opportunity to grab her) no longer makes sense. It just cuts to a scene of Dani suddenly outside the protective circle and screaming as Winnie swoops down on her from above. Without knowing about Dani retrieving Billy's head the viewer is left puzzled as to why Dani left the circle.

Edited into Hocus Pocus 2 (2022)