When Bob first arrives at the hotel he has the first button or two undone on his shirt with no t-shirt visible. When we see him in the elevator moments later, a white t-shirt is visible under his shirt.
Early in the movie, during her distress call home, it appears that Charlotte mentions she "even tried ikebana" (the Japanese art of flower arrangement), but in fact only does so later, while wandering about in the hotel.
During the still photo shoot, the photographer asks Harris to pause so he can change films. The assistant can be seen sliding the lightproof cover into the film magazine on the back of the camera, and then immediately removing the sliding cover, all without actually changing films or magazines.
In the karaoke room, a shot of Charlotte speaking shows the room number as 601. In the next shot, Charlotte is sitting outside the room, smoking, and Bill comes out of a door now showing 602 instead of 601.
When Bob lies alone near the beginning of the movie (just before he gets a fax), the clock reads 4:20 in a close-up shot. At the end of the following long-distance shot, the clock is blurry, but clearly changes (probably to 4:21). In the following shots, it's back to 4:20.
When John is about to go away, getting his jacket and approaching Charlotte who is on the bed, his hair is dishevelled. In the next shot (from the side) his hair is smooth. Then again dishevelled when he's at the doorway.
After the karaoke scene, Charlotte is in the hallway with zebra wallpaper. The first camera shot looking down the hall, shows Charlotte with her head against the dark painted wall. In the next shot looking directly at Charlotte and Bob, Charlotte's head is against the zebra part of the wall, however her position in the hallway has not changed.
After Bob and Charlotte come out of the arcade, their friend Charlie Brown calls them so they can get in a car. As they are getting in the car we see a man running down the street. In the next shot, he is gone.
When arriving in Kyoto, there is a scene of what appears to be a 700 Series Shinkansen arriving at the station implying that Charlotte had been riding the 700 Series. However, when Charlotte is shown walking away from a train, it is a much older 100 Series Shinkansen.
When Bob lays Charlotte on the bed after carrying her to her room, a few inches of stomach are visible between her sweater and skirt. When the camera cuts back to her, the sweater is pulled down and no skin is visible.
When Charlotte listens to the "find yourself CD" she is looking at the front cover, which makes the back of the cover visible to the audience. When she turns the box around, the back cover that she's looking at is different than the one we just saw.
In both scenes where John rushes out of the hotel room, a wood-textured door is visible immediately next to his door at a perpendicular angle. When Bob takes Charlotte back to her room after the first night out, the door he goes in is in the middle of a hallway.
When Charlotte is in the amusement arcade, she watches a boy playing an electric guitar game and smoking a cigarette. When the boy is facing the camera the cigarette is on the right-hand side of this mouth. It is on the left-hand side when the reverse angle is shown.
In the amusement arcade where Charlotte watches the boy playing the electric guitar game, a man in a red baseball cap walks away from the camera behind the boy. In the next shot (reverse angle) the man is seen playing an arcade game using an infrared gun.
The first time that Charlotte sits down with Bob at the bar, her lighter suddenly moves from on top of the pack of cigarettes to her hand when Bob lights the cigarette for her. After that, she puts down the lighter over the counter, a click sound can be heard. However when the camera switches back to the front shot the lighter is on top of the packet again.
When Bob is on the phone to Lydia after he gets back from karaoke, she tells him that the kids are eating breakfast and she needs to get them off to school. In reality, the earliest it could be is 11 am on the west coast (when not during daylight savings) if it's 4 a.m. in Japan. This is too late for breakfast if the children are heading to school.
In the opening scene when Bob Harris is arriving in his taxi, he is looking out the window at the bright lights of Shinjuku where his hotel is located. The one sign he notices however (the red bannered kanji with the blue circular lights) is a very distinctive sign located at Shibuya Crossing.
After their long night out performing karaoke with Charlie and his friends, Bob and Charlotte's taxi can be seen crossing the Rainbow Bridge heading east towards Odaiba. Odaiba is a man-made island located in Tokyo Bay. This is a pretty far detour from their hotel in Shinjuku. To get back to their hotel, they'd have to turn around and drive back over the Rainbow Bridge in the opposite direction.
In the scene where Charlotte arrives at Shibuya Crossing, the camera shot from her point of view suggests she is crossing away from Shibuya Station, viewing the dinosaur on the jumbo-tron across the street. In the shots where we actually see her crossing the street, however, she is instead walking towards the station.
Bob Harris (Murray) is shown at the very beginning arriving in Tokyo by car. Background sound at the start of the sequence includes a public service announcement identifying Narita Airport (East of Tokyo) as port of entry. The sequence ends with his car pulling into the Park Hyatt hotel in West Shinjuku. In between we are shown POV shots of Tokyo from inside his car, but they are shots which would be seen by someone heading east OUT of the West Shinjuku Park Hyatt area, not entering from east INTO the area. Arrival at Park Hyatt from either of Tokyo's airports would be straight off of Shinjuku's highway interchange, not passing any of what's shown. What's shown is the view from a car LEAVING the West Shinjuku neighborhood, driving east AWAY from Park Hyatt under the Yamanote train line into the bright lights lining Yasukuni Road where Kabukicho red light district begins in East Shinjuku.
When Charlotte takes the subway, the orange "you are here" circle on the map indicates that she's at Shibuya station. When she gets to the platform, a sign says she's at Omotesando station, one stop away on the Ginza line.
The closing sequence begins with a sun-RISE shot of Bob Harris (Murray) beginning an a.m. departure from the Park Hyatt hotel & Tokyo. But the iconic shot when he jumps from his car and embraces Charlotte (Johansson) on the street shows sun-SET lighting along that particular pedestrian street after only a few minutes of screen/story time have elapsed. Logistical discrepancies and position of the sun throughout that whole sequence are clear to anyone familiar with that Shinjuku location.
When Bob and Charlotte first see each other in the hotel elevator, a Japanese woman is seen wearing a kimono with the right flap covering the left. In Japan, this is only practiced with burial kimonos, indicating that the scene was most likely flipped.
At the end of the scene where Charlotte first sees Bob in the elevator, she does not actually exit the elevator. At the far right side of the screen, her purse is visible, revealing that she is just standing there.
After Charlotte injures her toe there is a shot of her sitting in the window. You can clearly see both of her feet including the toe that was injured (and later proved to be so bad that she needed to go to the hospital) but all toes look normal.