Tooms is released after a year yet his apartment has been demolished and a new building has been constructed in its place. It is unlikely such an intricate structure could be created and opened in one year.
In episode three of this series, when the sheriff sees the newspaper declaring Tooms has been sent to prison, he rips out the text, separating it from the photograph of Tooms. However in this episode, the sheriff is seen looking at the same removed piece, but with the photograph.
(In episode 3, you see the sheriff START to rip the newspaper. However, when they show it being separated from the picture, it's in Tooms' hand. He ripped it for his cocoon/nest. They never show how the sheriff rips the paper, he could have very easily torn the paper across the top of the article. This would have made the tear go around the article and not through it. The sheriff going around the article makes more sense since he told Fox & Dana that he had waited for 25 years for someone to ask him about the case.)
A body encapsulated in cement would remain conserved in a relatively good condition. The remains found in the concrete floor however, consist merely of bones.
When the police come to Mulder's home, they enter without asking his permission, and seize evidence without presenting a warrant.
In the scene with Tooms' dental radiographs, an anatomical "full mouth series" (FMX) is depicted, however all of the films are in a random order, not anatomically correct.
When the victim enters his car, it is shown from Tooms' mutant vision perspective, where only the target is in color and everything else is not. In the previous scene - as the guy was walking to the car - it was indeed red.
As Mulder enters the escalator shaft to search for Tooms, you can see the reflection of a red LED on the filming camera reflecting off of polished metal surfaces.
Twice we see Tooms being alerted by someone wearing blue (a woman in a blue coat and a man in a blue suit) as possible prays so much so that the rest of the image around these two characters turns black and white. Still, at the end he will jump on the psychologist not wearing anything blue, that he knows for years and in its room which will direct any suspicions towards him who is supposed to be so careful.