Mulder: It's been said that fear of the unknown is an irrational response to the excesses of the imagination, but our fear of the everyday, of the lurking stranger and the sound of footfalls on the stairs, the fear of violent death and the primitive impulse to survive, are as frightening as any X-File...as real as the acceptance that it could happen to you.

Scully: You think you find a way to deal with these things. In med school, you develop a clinical detachment to death. In your FBI training, you are confronted with cases, the most terrible and violent cases. You think you can look into the face of pure evil. And then you find yourself paralysed by it.

When Scully pushed Pfaster into the bath tub, his left arm was wet to the elbow. But, in the next scene, he was dry.

Donnie Pfaster is going through the city, looking for a prostitute, when a bus passes by, with the destination sign reading, UBC. The University of British Columbia is in Vancouver, but this episode is supposed to be set in Minnesota.

Scully dates her autopsy November 14th. We learned that the episode "3" occured during November, which would mean that "One Breath," "Fire-Walker," (where Mulder and Scully were supposed to be quarantined a month at the end) "Red Museum," "Excelsius Dei," and "Aubrey" all occured in less than two weeks.....

"[T]his kid in Milwaukee": Jeffrey Dahmer
Agent Bocks tells Mulder about why he thinks it took so long to catch, "this kid in Milwaukee." The person in question is Jeffrey Dahmer, who was apprehended by police on July 22nd, 1991, in Milwaukee, Wisconsin. Facing charges of killing seventeen, he plead not guilty by reason of insanity due to his predisposition to necrophilia. He would later be found guilty of killing and dismembering fifteen people and was committed to the Columbia Correctional Institution in Portage, Wisconsin. On November 28th, 1994, less than two months before this episode aired, Dahmer was confronted by an inmate and beaten to death. More information about Jeffrey Dahmer can be found here.

Creator Homage
The football game shown in this episode between the Minnesota Vikings and the Washington Redskins was made up of one Carter on each team. As a homage to series' creator Chris Carter, during one play the name Carter can be seen on the back of the jersey of the Minnesota Vikings receiver. The receiver's name was Cris Carter, who played for 15 years for the Philadelphia Eagles, the Minnesota Vikings, and Miami Dolphins.

11:21 Redux II
When Mulder calls Scully up to tell her that they found a dead body, she notes the time as 11:21. As in the "Pilot" and "The Erlenmeyer Flash", it is a reference to November 21st, the birthday of Chris Carter's wife, Dori.

"She was Scully. Like that baseball announcer.": Vin Scully
Pfaster's question about the agents' names to his cellmate prompts the man to tell him that Dana Scully has the same last name as Los Angeles Dodgers' baseball announcer Vin Scully. In fact, Chris Carter gave the character her last name as a tribute to Vin Scully.