The Cessna Skyhawk seen has a USA "N" number, but later it is seen with a Canadian "C" number.
A Northville, NY police car has red and blue emergency lights mounted on its roof. Per New York State law, police and emergency vehicles may only have red and white lights visible from the front and sides.
In the briefing scene following the crash, Mike Millar refers to "Dr. Spock's phaser." Dr. Benjamin Spock is a famed pediatrician. Mr. Spock would be the person using a phaser and is a character from Star Trek (1966). Although someone like Mulder would never make a mistake like this, Mike Millar has been established as not having much interest in "far out" stuff, and this is possibly a deliberate character error by the producers.
When the body of the assassin is uncovered at the crash site, the actor is obviously breathing and his pulse is visible in his neck.
Mulder and Scully are celebrating her birthday (February 23) at the beginning, but when they go to the plane crash site, the time is listed as 5:52 AM in very bright sun. 5:52 AM in February in New York State would still be predawn and very dark.
When preparing to dive to at least 50 feet, Mulder admits to never having scuba dived before. Diving to that depth with no knowledge of how to operate the equipment nor how to breathe with the regulator, would be a likely death sentence.