In "Monday", Mulder's Omega watch displays the time and the day of the week. In Arcadia (1999) it displays the time and the date.
When Skinner approaches the lead cop outside the bank, Skinner asks who's in charge, to which the cop says "I am, unless the Bureau wants to take charge". By law, all bank robberies are the jurisdiction of the FBI, being federally insured by the FDIC. Skinner should have taken charge until properly relieved by an appropriate Special Agent in Charge (SAIC).
Mulder's waterbed is shown with a
leak spraying water in the air. This might happen if one or more people were lying on the bed or pressing down on the mattress, but the fountain continues to spray when he is out of the bed. Waterbed leaks don't spray so much as ooze. Furthermore, the amount of water lost to cause the degree of saturation on the carpet (not to mention leaking into the apartment below) would mean that the bed would have lost most or all of its water, leaving Mulder waking up lying on the bottom of the mattress box.
The episode takes place in Headquarters in Washington DC but in the scene when Mulder is walking to the bank, Los Angeles City Hall is clearly shown in the background
Mulder's paycheck lists his home address in Alexandria, VA with zip code 23242, but that zip code is for Henrico, VA, which is right outside of Richmond, VA, instead (101 miles apart).
In the final scene, a newspaper headline reads, "Dogs Spread Flu Epidimic." The word "epidemic" is misspelled.
At the 44 minute mark, Scully, as a medical doctor, should prioritise the shot 'patient' (Pam) - yet she runs outside to call emergency services instead and leaves her to die.