Dr. Phibes speaks without being hooked up to his vocal apparatus in several scenes in the film, suggesting that dialogue was added later. This is especially noticeable when he addresses his dead wife while moving her coffin into the tomb in Egypt.
As Phibes waits to take the barge down the river, a large circular window frames his head in closeups. In long shots, there is no window anywhere in the wall behind him.
(at around 49 min. into the film) You can see the logo Dr. Phibes' Clockwork Wizards on the front of the bass drum (this can be seen better at around 52 min. into the film). It stays this way until 1 hr. 10 min. into the film. Then it says The Alexandrian Quartet.
When Hackett finds the mannequin Fusseliers, some are obviously moving against the wind, showing that they are men in costumes trying to remain motionless.
When Ambrose looks at Victoria in her glass coffin, she is visibly moving.
At the end of the film, which takes place in 1928, Phibes sings "Somewhere Over The Rainbow", a song that was first recorded in 1938, 10 years later.
(at around 47 min. into the film) Biederbeck says "Understand that I will give the orders," but his lips do not move.
When Hackett returns to his truck after being tricked into thinking soldiers are nearby, several members of the camera crew can be see reflected in the truck's bodywork on the left of the driver's cab.
When and how did Phibes bury the body beneath Diana's tent in the middle of a busy camp?
In the film's final scene, Darius Biederbeck begs Phibes to take him to the River of Life, but Phibes ignores him. Seconds later, the elixir Biederbeck had been using to stop him from aging wears off and he rapidly ages and dies. This makes his pleas totally irrelevant. If Phibes had decided to take Biederbeck with him, Beiderbeck would have died on the way.
(at around 35 min. into the film) When Phibes and Vulnavia are unveiling the clockwork musicians, he mispronounces her name as "Vulvania".
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 has 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.