In the supermarket scene Agent Scully buys pickles and ice cream. This is an in-joke as Gillian Anderson was pregnant at the time.
When Duane Barry is seen on the alien's exam table it is set up to look like Leonardo Da Vinci's "The Vitruvian Man".
David Duchovny declared that Mulder wears the acclaimed Speedo in the scene at the pool at his suggestion to Chris Carter. Carter wanted Mulder to be wearing a typically long Californian surfing suit, but Duchovny thought that Mulder would not be doing pool laps in such a suit.