The condition of Felix's teeth change drastically between 2 scenes that took place on the same day. In the scene where Felix and Ned get married when Felix smiles his teeth are grayish in color and noticeably decaying, but in the scene right before that when Felix goes to see Ned's brother to discuss his will his teeth are whiter with no signs of decaying.
In "Men's Country" scene, when Ned gets in his room, the hinges of the door are on the right side; when Felix followed in, the hinges are on the left side.
When Ned is in the doctor's waiting room he picks up a copy of Time magazine. The cover mentions Vietnam veterans, this was indeed the subject of the Time July 13, 1981 edition, but the cover design has been altered.
When Felix is riding the subway while observing a rider with lesions, the subway car is immaculately clean and graffiti free. During the early-1980s (the time this film takes place), New York City subway cars were notoriously gritty looking with graffiti covering the inside and outside of the cars. Police officers were also a common sight as crime on the subway was at an all time high. During the late 1980s, the Metropolitan Transportation Authority (MTA) which oversaw the city's subway services purchased a newer model from Canadian manufacturer Bombardier that was made of graffiti-proof alloys and had a different seat layout from previous trains. This model is the one used in this film.
When Ned and his friends are trying to collect money for "Gay Cancer" in the park, the 3 quarters one donor throws down are all from the State Quarter Series, which was begun by the US Mint in 1999.
The clock tower seen across the Hudson River (in Hoboken, NJ) was not standing in the early 80s when the film's story took place. It was demolished in the 50s and rebuilt in 2007.
In the house at Fire Island a Baseball game is seen on the TV which Bruce mentions. In the summer of 1981 however there was a long MLB strike from June 12th through August 9th, 1981 during which time that scene presumably is set and no games were played.
When Dr. Emma Brookner (Julia Roberts) delivers her monologue requesting funding for her research, she says, "A promising virus has been discovered in France," when, presumably, she means a promising "vaccine."