When Sara is having a conversation with the guy who cleans up the ballroom where Jonathans wedding supposed to be, Sara has a small spot of sweat on the back of her shirt. In the next shot the spot appears to be much larger.
Jonathan Trager (John Cusack) calls Dean Kansky (Jeremy Piven) "Gerald", Cusack's real life pet name for his life-long friend Piven. In mitigation, this could be considered Jonathan's pet name for Dean, an in-joke rather than a goof.
When in the opening scene when Jon and Sara are fighting over the gloves, the older male shopper says that it is five days before Christmas. However, when Jon finds the receipt years later the date is 12/21 which is only four days before Christmas.
When Sara is watching her fiancé perform in a bar, her shirt reaches down to her waistline. Shortly after, when she goes through Chinatown during heavy rain, her shirt shows her belly and belly button.
When Sara crosses the street to buy the Certs, she approaches and you can see the stand employee grab the five dollar bill out of Sara's hand. When the camera angle changes, Sara sets the five down on the counter, and then the man behind the counter picks it up.
When Jonathan and Halley are in the apartment and the smoke alarm goes off, Halley jumps up, and Jonathan settles himself down on the bed, unearthing the red Bloomingdales bag containing the glove. When you see the bag come into view, Jon's holding a television remote in his left hand. When he picks up the bag and sits up, the remote has switched to the right hand.
The ferry that Sara is riding from San Francisco Ferry Building is seen moving left to right across the screen with the Bay Bridge in the background. This is the direction ferries travel on the way to San Francisco.
At the end of the film, the leaves on the trees are clearly green, meaning that it is at least the end of May, yet it snows when John and Sarah meet at the skating rink. This is essentially impossible.
The $5 banknote with Jon's name and phone number is shown three times in the film: On the first evening, when Jon initially labels the banknote, years later when Eve gets the note as change and the following day when Sara uses the note to pay on the plane. The inscription varies slightly from scene to scene. This can be explained as a simple requisite error or tells a detail of the story which is not shown in the film: To increase his chances Jon may have labeled many more $5 banknotes and passed them on.
Towards the end of the film a remark is made about "what happened to Spring?" referencing the rather mild weather. This scene appears to have been (re-)shot during the warmer months as many of the locals in the distance are wearing shorts and T-shirts yet everyone in the foreground has a few layers on (though not too many to appear ridiculous), however it's snowing later that day (or the next).
The goof item below may give away important plot points.
There isn't enough time for Dean and Jonathan to travel from New York to San Francisco at night and return to NY by noon the following day to attend the wedding. Typically, the last flights from NY to the west coast leave around 8:30 p.m. or so and there wouldn't have been enough time for the guys to get to the airport following the rehearsal dinner. Also, because of the time delay, they wouldn't have been able to get a flight from SF to NY the following day to make a noon wedding, no matter how early they left SF. A red-eye would be out of the question, since a red-eye would have left around 10 or 11 p.m. the night before - which is when their flight from NY would've gotten in.