When Trout and Waverley stop their car in the desert to consult a map, Waverley points left and states that Cairo lies in that direction, then points right and says that the Red Sea is in that direction. Cairo is west of the Red Sea, so logically he's just pointed west, then east. Waverley then looks forward and tells Trout that England lies that way. They are actually looking south, with their backs to the correct direction.
Dr. Phibes speaks without being hooked up to his vocal apparatus in several scenes, suggesting that dialogue was added later. It's especially noticeable when he addresses his late wife while moving her coffin into the tomb in Egypt.
The opening scene, where Dr. Phibes' blood is pumped back into his body, is clearly reversed footage from the end of the first film. The "blood" jumps from the bottom of the jars to the ends of the tubes at the top, and flows against gravity.