Factual errors: Suzanne Modeski asks Byers to help her decode a printout of an encrypted file. However, since almost all file creation and encryption systems make extensive use of non-printing characters (especially for the type of printer used in the episode), it would have been impossible to decipher the information on the paper.
Continuity: During the shootout scene in the warehouse towards the end of the episode, Mulder is wearing a wedding ring. Since this episode is set in 1989, it might have been possible that Mulder was previously married except that, earlier in the episode, the Lone Gunmen hack into the FBI mainframe and Langly reads out Mulder's Dossier which clearly states that Mulder is single.