When the guard, Pierce, comes into the office and sees the leftover sandwich and banana he is alerted to something being wrong. However, later when Dr. Staple comes into the office - the food is gone from the desk. It is unlikely that Elijah took the time to clean up whilst reprogramming the computer system.
In the Guard Office, a large wall calendar shows June with 9 days "X"ed out, but a couple of days later, characters are sitting in a train station with a decorated Christmas tree in the middle of the station.
Elijah's scars are shown as a long line with several small lines crossing over it at regular intervals - these are meant to depict sutures from a surgery. However, an actual scar heals as a line bordered by dots, as only the places pierced by the needle would leave a scar. It is only suture material that crosses perpendicular to the original trauma line, which would leave no lasting mark.
Ending scene, when the 3 "remaining" characters are awaiting for the people's reaction in the train station, Mrs. Price starts to hold the hands of her 2 fellow survivors, and the coffee cup she was just given by Joseph seconds before has totally disappeared.
Joseph mentions the "mutilations at the zoo," that is, the events seen in Split, as taking place "three weeks ago." Also, several times it is mentioned that the crash of Eastrail 177 was nineteen years ago. But at the end of Split a diner patron mentions Mr. Glass having been put away FIFTEEN years before (which was closer to accurate at the time of release). Since the train wreck and Elijah's capture were only a few days apart, both timeframes cannot be true.
Mr. Glass' computer code is on screen long enough that it's clear that it is actually an example from a programming tutorial, complete with detailed comments explaining basic concepts in the programming language in question.
The goof items below may give away important plot points.
Daryl parks in front of the hospital before his shift the night Mr. Glass sets his plan in motion. The next morning when Dr. Staple arrives, Daryl's car is gone. Daryl did not leave the hospital; he was killed by Mr. Glass that night.