Other mistake: At Natalie's house, when she is leaving and Lenny is taking a picture of her, the background looks totally different than from what is shown on the picture: the curtains are opened wider, the door is half open, there is a lamp on the left and there is no mirror on the wall. (00:17:10 - 01:20:50)
Other mistake: In the scene where Leonard finds Dodd, he calls Teddy. When Teddy knocks at the door, Leonard goes to answer it. Just as he's about to open the door, there's a dodgy edit and you see Leonard jump to the left a little. (00:41:20)
Other mistake: In the Sammy/Lenny shot in the Institution, before the switch the orderly on the left heads toward the medical files with his arm outstretched and the nurse walks behind Sammy. Just as the person passes the camera the film jerks and the two men at the table, visible on the left, have a shaking motion. After the switch, the orderly and the nurse are both further back. (01:29:50)
Answer: The are no alternative endings for this film, all that is on the third disk is the movie played in chronologial order so you can see how things really panned out.