Both times the main characters drive to the old mission, the wide shots show them driving on the right side of the road. However, all shots inside the car show them driving on the left side of the road. This is because the US 101 - where filming took place - near San Juan Bautista is split, with two lanes in each direction, by a grove of Eucalyptus trees. The film shows only one of the road's directions, giving the appearance that Scottie and Madeleine are driving on the wrong side of the road.
As Madeleine leaves the florist in her Jaguar, Scottie follows her in his 1956 DeSoto, with license number HAF 376. However, 54 minutes into the movie, he follows her again, but the camera car, a similar DeSoto, with Scottie at the wheel, passes the HAF 376 licensed DeSoto which is erroneously parked at the curb.
Scottie is standing on the top of a step stool when he faints and falls. In the next scene, Midge catches him after he falls only about one foot. Based on the height of the stool, he should have fallen at least three feet.
When Madeleine is in Scottie's apartment after he rescued her from the bay, he offers her two cushions to sit on in front of the fireplace. When he picks up the cushions, they are green. In the next shot, when the cushions are shown hitting the floor, they are gold. When the cushions are shown lying in front of the fireplace after Madeleine has fled, they are green again.
During the opening scene when Scottie hangs onto the rain gutter, the tiling of the roof top he slid down changes from flat wooden tiling to half-cylindrical brick tiling when the police officer returns to try save Scottie. Close-up shots of the police officer show half-cylindrical brick tiling, whilst the medium shots with the officer and Scottie hanging on, show flat wooden tiling.
When Scottie buys Judy a flower from the street vendor across from Ransohoff's, they cut to a studio closeup of them that includes a large bunch of purple carnations which Judy brushes against as they leave, but when the scene returns to the location shot, the flower bunch is nowhere to be seen.
The DeSoto that Scottie drives clearly has no rear view mirror during the close-up and interior shots, yet it has a rear view mirror as he's getting back into the car after watching Madeleine Elster purchase the flower bouquet and as he exits the car on the passenger side to follow her into the Mission Dolores cathedral.
When Madeleine walks out of the Art museum and continues on to throw flowers in the bay before she jumps in and is taken out of the water by Scottie, she has no purse. After she wakes up at Scottie's and puts on his robe whilst her clothing is drying, she asks for her hairpins and purse which he brings to her. Perhaps, she left the purse in the car when she jumped in the bay, but most women would not go into a museum dressed in a suit with gloves and leave their purse in the car.
As Scottie parks alongside Madeline in front of his apartment, his car (actually the camera truck) cuts across several parking spaces. When the angle changes and Scottie is shown stepping from his car, it is parked within one parking space.
After Madeleine has talked to Scottie outside his flat and got into her car, a pedestrian is just about to cross the street in the background. The camera cuts back to Scottie following her immediately, but the pedestrian has disappeared.
As the camera moves away from Scottie standing at the edge of the tower, the shadow of the camera can be seen for a split second on the outer wall of the tower. On the Alfred Hitchcock Masterpiece Collection DVD, the image is cropped so the shadow cannot be seen.
A hand mysteriously rises from behind a gate over James Stewart's left shoulder (as he follows Kim Novak) and waves at the camera, about 55 seconds into the Mission Delores graveyard scene.
Maybe it was on purpose to create more of a Madeleine Spirit by Hitchcock?
Carlotta, Madeleine's great grandmother, was born in 1831 and died in 1857 as indicated on her gravestone. This would place her grandmother's birth at around 1850, her mother's birth at around 1870, and Madeleine's birth around 1890. This would then make her around 68 years old when the story takes place, instead of the 25 or 26 that she is supposed to be.
Madeleine enters her hotel without being seen by the desk clerk, and disappears from her room only moments after Scottie sees her standing in the window. The audience is allowed to believe that this is a manifestation of the supernatural, specifically Madeleine's possession by a dead ancestor, but that is later proven to be untrue.
When Scottie buys new clothes for Judy at Ransohoff's, Judy is shown trying on a pair of shoes. Due to the extremely low camera angle when Judy walks away from the camera, it's easy to see that the shoes are not new- their soles are heavily scuffed.
When Madeleine arrives at Scottie's apartment to post a letter, the establishing shot shows only a few bushes by the metal railings. However, in the closer two shots, more bushes are can be seen against the railings.
Madeleine enters the McKittrik Hotel and the sky is overcast. When she appears in the window of the 2nd floor room, she is clearly illuminated as from sunlight, throwing a distinct shadow against a light background, whilst the rest of the shot remains illuminated modestly (possibly assembled footage).