Mulder wears glasses when he first starts scrolling through the microfiche to find out about Tooms; but later scenes don't show him wearing them. Since he doesn't wear them for driving, we are led to believe they are for reading, but he doesn't use them more than once.
When Tooms is in the cell right at the end, we see when his food is being brought over to him on the tray that there is a drink and a bun, when the shot changes to the other side of the door the drink and bun have swapped sides. When the shot changes back to the other side of the door, the tray is now the other way around and then when the shot goes back to the other side the whole tray has now disappeared.
Towards the end of the episode, when the retired police officer is reading the newspaper, the third column in the article on Tooms' capture is a repeat of the text in the lower portion of the second column, in the middle of the paragraph "Tooms, who apparently broke and entered the home early Tuesday evening, attacked Agent Scully when she arrived there a short time later."
When Mulder is comparing Tooms' fingerprint to the one found in Usher's office and stretches the current one like the older one, they are exactly the same. This would be extremely unlikely since the angle and amount of pressure would have to be identical.