When in the first scene, Julia Govern's killer puts the phone in her hand, her hand is on her leg. In the photos that Ward shows to Bower, Julia's hand is on the ground and the phone is not in it. A little later, when Michael remembers the crime scene, Julia's hand is on the ground and the phone is in it. If for any reason Julia's hand has fallen to the ground after the phone being placed in it, it is very unlikely that the phone will remain in it.
When the audience see Diana's home for the first time, she gives her cat a bowl of milk and some food. When she goes outside in the next scene, the camera pans back to her cat and, although the cat's food dish is still there, the bowl of milk is gone.
When John Doe (Michael Winslow) is researching on the internet (01:03:41) one of the victims details is given as so "Eileen Lee's body has been found in the outskirts of Dallas on June 31th" . June has only 30 days (01:03:41). Additionally, day 31 of a month always has an ordinal suffix of st, not th (i.e. it should be 31st).
About 87 minutes, "Frank Ward" (Malik Yoba) appears to take a drag on a cigarette. However, you can clearly see the "hotbox" is simply a bright orange tip on the end of it (not lit).
When Oliver has Michael in the basement he says "I'm sick John. I know I am" The characters name Michael, the actors name is John. He called him by his real name.