Revealing mistake: At the 'beginning' when Teddy and Leonard drive up to the abandoned building with the old truck out front, inside the truck Leonard handles a number of .357 revolver calibre bullets that have apparently not been fired, but you can clearly see the indented primers in the base of the bullets, indicating that they are just inert movie props. (00:04:40)
Revealing mistake: At the diner Teddy puts his fingers on Leonard's pulse and Teddy's watch reads 4:45. Teddy jokes that Leonard probably left his key in his room. Leonard goes back to his motel to find his key and asks Burt for the time, to which Burt replies, "A quarter to one," - 12:45. (00:24:25 - 00:26:20)
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.