At the end of the movie, when the survivors place roses in front of the house, the roses intersect each other at about the middle of the stems. The next time the roses are shown, the point of intersection is much lower.
When Joyce Reardon is teaching her class and is probed by Kevin Bolinger, he claims he is "class of '03". The subtitle at the beginning gives the year as 2001, ten years after Annie's 1991 incident with the dog, and yet, when Bolinger is dropped off at Rose Red by Professor Miller, Miller tells him he will be out in the real world "in a matter of weeks", as if he stood to graduate.
When they're in the hallway Sukeena designed, Prof. Reardon says that Ellen Rimbauer disappeared on Jan. 15th, 1950 when she was 70. She couldn't have possibly been 70, because earlier in the series, Prof. Reardon stated that Ellen was 20 in 1906 when she got married.
After Annie falls and hurts her head, the bandage that is placed on her head is white in one scene and has a blood spot and back to clean in the next. It alternates several times between scenes from clean and the blood spot.
When Dr. Reardon dismisses the class, Professor Miller can be seen leaving the sound room (upstairs); when Bollinger gets up and goes to talk to Dr. Reardon, Professor Miller is seen still standing in the sound room as if he never left.
The main story is set around Memorial Day, which is in late May. But Annie's Dad and the psychics at the bar have the same thing on TV; a Washington Huskies football game. College football season is September to January; there's no football in May.
Though the house is protected by a gate that only seems to be operable using a remote control (as in a later scene there is no signs of an intercom), a pizza delivery man seems to have no problem getting to the front door of the house.
The group goes to visit "Rose Red" on Memorial Day weekend, which is at the end of May. The shots taken outside during the movie show the leaves all off of the trees and all over the ground in autumn colors, and there is a football game on TV, suggesting that it is more like October.
The goof item below may give away important plot points.
When Emery's mother is tied up in the kitchen in the 3rd part, after she sees the two figures upside down the camera pans away and shows a towel or sheet folded under her head. Moments later the lady with the man in the kitchen takes the same towel/sheet off the table and puts it under Emory's mothers head.