Joseph Cotten would grumble on the film's set that he had to remember and deliver lines, while Vincent Price's were all to be post-dubbed. Price responded "Yes, but I still know them, Joe." In fact, Price was well-known in Hollywood for his ability to memorize all of the characters' lines in a given production, not just his own.
In the film's original script Phibes was abusive to Vulnavia, eventually stabbing her to death and then escaping his house (which was to catch fire) in a hot air balloon with Victoria's body. It was decided to make Phibes a more sympathetic character, so these scenes were cut.
For visual reasons the plagues of flies and gnats were replaced in the film with rats and bats.