As Ray is eating his sandwich it goes from having aluminum foil, not having the foil, and then back to having it again. Also the first bite mark changes. When Ray is filmed from behind the sandwich has a bite on only one slice of bread.
Just after Scully has completed the autopsy, Doggett comes in to tell her that Ray's print has been found on the car, and that blood found there is also a match to his. Not only does this seem an inordinately short time to complete a DNA match, but there's no evidence that they ever had anything to compare the blood to, so how do they know it's Ray's?
How can a shotgun shot throw Ray out the window, where a moving car didn't move him an inch ???
The movie staple of people being thrown backward when shot with a gun is a myth - this fact also supports this users comment.
Doggett: What are you saying? Ray Pearce has become some kind of metal man? Because that only happens in the movies, Agent Scully.
The soundtrack features a repeated theme from the first movement of Grieg's piano concerto.
The 4-door 1973 Ford Torino destroyed in the episode is the same vehicle owned by The Dude in The Big Lebowski. The car was used in the film before use in The X-Files.
The scene in which Ray was poking at his face in front of a mirror under the flickering bathroom light is very similar to a scene in 'The Terminator'. Robert Patrick starred in 'The Terminator 2: Judgement Day', ironically as a man made of metal.
Agent Doggett comments that you can only see metal men in movies; a reference to him playing the liquid-metal T-1000 in Terminator 2 - Judgement Day.
The plot of a "monster" getting back at its "creators" follows along the lines of Frankenstein and his monster.