Scully and Mulder's bickering during the episode - over Mulder's "ditching" Scully, how Mulder always drives, how Scully's feet are small, etc. - was derived from fans' online complaints dating back as far as the beginning of the series.
Syzygy is a straight line configuration of three celestial bodies. Syzygy is also a term used by Carl Gustav Jung to mean a union of opposites.
Gillian Anderson thought the dig at her height when Mulder remarked that he usually drove because he didn't think her feet could reach the pedals was hysterical. This was borne out of much online speculation as to why Scully never drove. Anderson is 5'3" (1.60 m).
The script originally called for the TV to be playing nothing but A Clockwork Orange (1971) on it. The rights to this proved too expensive so footage of the Keystone Kops was used instead.
This episode split fans. Some were opposed to the idea of Mulder and Scully being so hostile to each other (due to a planetary misalignment), while some loved the caustic banter between the two. Of the two groups, some of the latter had t-shirts with the episode's catchphrase printed on them: "Sure. Fine. Whatever."