Continuity mistake: When they give Garber the pistol to take, it has actually changed when he pulls it out of the bag, it's an entirely different pistol.
Continuity mistake: Towards the end of the movie when the single train car is rushing down the Coney Island bound F line, you see different camera shots of the train above ground. One of the shots shows the train speeding past Shea Stadium, which is actually located in Queens on the 7 line.
Continuity mistake: When Ryder first walks into view over the Internet feed from the laptop, he is wearing a greyish T-shirt (most likely short-sleeved as well). In the next shot, still on the feed, he's wearing a black leather jacket, the same one we see him wear since the beginning. (01:01:20)