When Salvatore Pucci (William Smithers) approaches Mannix during the last rites scene in Rico Pucci's bedroom there are tears shining on Smithers' face visible in the medium shots taken from Smithers' right, but they disappear in the closer shots taken from directly in front of him.
At about 9 minutes, when Mannix sees he is being followed the car behind is seen in a rectangular side view mirror. But the side view mirrors on Mannix's car are round shaped.
No one in the Church, especially a bishop, would hire a private eye to investigate a possible miracle. The Church maintains professionals who investigate all reported miracles. The investigation is extensive and leaves no room for doubt.
When the camera shows the mirror view of the car following Mannix (with the incorrect rectangular shape), the image is not reversed as it should be in a mirror.
Sandy (Brenda Scott) picks up the phone, presses a line button, and calls Kiley (William Bryant) to tell him Mannix is waiting, but the light for the phone line doesn't illuminate.
Stanley Blake is shot in the left portion of his chest. At the time, he is standing behind Mannix, who has turned to go to his car. From their positions, there's no way the bullet should have missed Mannix.