When Sydney and Jack are talking about Will on the cliff, Sydney says that the blank page is with the CIA and the ampule is with SD-6. In fact, it is the reverse situation--the ampule is with the CIA and the blank page is with SD-6.
Emily's wine glass goes from half full to 3/4 full from the point Arvin gives it to her, and the point at which she drinks it.
Jack tells Syndey that she only has 57 minutes until the passwords are changed. Since she took passwords in the middle of the day and used them during the night, certainly more than an hour has passed.
The recap for Rendezvous (2002) shows Sydney telling Will "If you need anything there are agents behind that mirror," but the scene was never part of the actual episode.