When Jeff visits Leonard Eels' office building, there are clearly five names on the directory under 'E' in the long shot, but just two in the POV shot that follows immediately.
When Jeff is at Whit's gate getting ready to go in, there are two large dark stains on the bottom left side of his coat, but later on, when he is at Eels' place, the stains are now gone.
When Jeff looks at Ann as she drives away from Whit's place he is standing at an angle perpendicular to the gate, but on the next cut he now has his back to the gate.
The sign on the Mason Building has an upside-down letter S. It was a back-lot building, so presumably it also shows up in other movies.
Joe pull into Jeffs station to stand behind the deaf kid repairing a tire. After not getting a response to his whistle or horn he lights a cigarette and throws the match where it bounces off the tire. Kid would have noticed someone was in the vicinity from smelling if not noticing the smoke cloud.
When Jeff drives up to the cabin to meet Kathie, he says it's getting dark, and as he turns off the main road into the forest, headlights are shining on Kathie. However, minutes later, after Fisher is dead, Kathie leaves with the car and there are no headlights on to guide her through a supposedly dark forest. In actuality, it was probably filmed in daylight then filtered to look dark, but someone forgot to show the headlights that were needed in the false evening.
At the end of the movie when they are making their get away the woody they are in changes to a sedan when it crashes into the truck, the spotlight is missing then the woody is shown after the crash complete with spotlight.
When Jeff and Kathie approach the cabin and open the door, the entire cabin is very brightly lit. But when Fisher shows up and all three are inside, the cabin is now quite dark. There was a fireplace going but it could not have emitted enough light to have lit up the entire cabin so brightly.
When Jeff is walking away from the lake, his fishing rod has a missing reel.
Leonard Eels' apartment at 114 Fulton Street would be part of the block then occupied by the main branch of the San Francisco Public Library (now the Asian Art Museum).
After Stefanos realizes Jeff has something to do with the disappearance of the corpse of the attorney he killed, he asks Kathie, "Where's Bailey?". But Stefanos knows Jeff by his original last name of Markham, he only briefly learned he goes by Bailey now, so there's no reason for him to call Jeff by that name, especially in a tense moment.
The deaf kid at the gas station is reading Joe's lips while being questioned, but Joe has a cigarette in his mouth most of the time. A cigarette in the mouth would make it very hard to read lips.