Other mistake: When Neo is running along while shooting, it switches to a shot of a soldier firing a shotgun. Just before Trinity kicks it out of his hands, he's firing at the same spot over and over. Trinity is behind him, and Neo is moving, so what is he shooting at? (01:38:45)
Other mistake: The guy says "looks like I'll have to send more flowers" then opens up the activation card and code to destroy the building. The code is 50617 but he swipes the card then pushes 50671. (01:00:00)
Suggested correction: If you watch the keys again he presses the exact appropriate numbers in order. 50617.
Other mistake: When the agent shows the spiral for the pattern of the messages, the spiral goes through South America and America. But the agent, before, showed two messages that aren't in the pattern; one in England (Stonehenge), the other in Cairo, Egypt.
Other mistake: In the ending credits, Keira Knightley's first name is misspelled "Kiera."
Other mistake: When Woods gets shot by the nails fired by the small robot, the amount of blood in his sweater keeps changing during the following scenes.
Other mistake: As the tarantula approaches the first small desert town (when Lovelace orders Grant to surrender the government to him), look at the townsfolk. Not one of them pays any attention to the noisy, giant metal spider as it lumbers towards the town. In fact, none of them react at all until the first building explodes. I guess giant spider robots were a common sight in the middle of the 19th century West.
Other mistake: When Sly hypnotises the guy, he tells him to wiggle his tongue. He starts wiggling his tongue exactly when Sly says, "Wiggle."
Other mistake: It's reasonable to assume that the house can hide small things like posters and even shelves when projecting images on the walls. When Ben's two friends arrive for the party, one of the walls shows an image and the couch disappears, and that's just way too big of an object to simply phase away, given what we see that the house can do.
Other mistake: When SETH goes to plant his miniaturized brain in a body, the body enters with close-cropped hair, the surgical procedure shows a bald head, then SETH comes out with the close-cropped hair again.
Other mistake: Lieutenant Fredricks introduces himself to Agents Riley and Baker as "Lieutenant Fredricks," and that's the spelling on his uniform's lapel. However, he is listed as "Lt. Fredericks" under the cast. (00:57:37 - 01:27:07)