Rob Morrow's (Jeff) hairstyle changes slightly between shots when he visits his mother; when he appears outside of the house (after storming out following an argument with his brother) his bangs are longer and 'up' whereas in the previous shots they were shorter and down on his forehead.
When John pulls into his driveway early in the film, there is another car parked in the street directly in front of his living room window, but when he goes in the house and walks directly to the living room, you can see out that window and there is no car there.
At the restaurant when Beatrice orders a martini with two olives she is chewing food when the previous scene shows she had not yet bitten into her food.
The "original" baseball card that Jeff tells John is worth $50,000 clearly has the words "Reprint Series" visible on the back, which means it wouldn't be worth more than one dollar in 1996.
When John is reading his mothers transcript of the story she wrote in her youth we see that she has misspelled the name of the Whitman's candy company as Whittman.
John is driving out of San Francisco over the Golden Gate Bridge supposedly in the evening. However, traffic is heavy going in while outbound traffic is light, indicating that it is actually the morning commute.
Although John and Beatrice have a breakthrough in their own relationship, the connection to John's failed marriages is never made, which was the whole point for his coming to stay with her.
John is a vegetarian who insists on shopping for groceries according to his strict beliefs, yet when he eats sandwiches they are on bleached, white bread.