(at around 9 mins) Mulder and Scully investigate a washing machine. Scully has a huge torch. After the cat jumps out, Scully's torch becomes just pocket-sized. Previously when Mulder and Scully enter, both have large torches. Prior to the washing machine scene, Mulder's torch also becomes pocket-sized.
When the deputy pulls the Shipley jersey out of the drain at the Shipley house, the name is visible. As he turns it around to inspect the front, it shows the name on the jersey again.
At approximately 1:46 in the teaser when the tentacle is coming up through the drain there are bars missing from the drain grill. Seconds earlier when water is coming up through the drain the cover had no missing bars.
Scully says she has never delivered a baby. While this might seem unusual to some viewers, given that she is a physician, it's entirely plausible that she may not have had the opportunity to perform or assist with a delivery during her medical training. Normally this would be an experience she would gain as a medical student (not necessarily as an intern, as has been erroneously noted here before); however, it's possible that all deliveries she might have had an opportunity to witness during her time as a medical student were actually performed by Ob/Gyn or Family Medicine residents, especially if she was training in a program where the delivery "numbers" were low enough that they had to be prioritized to residents and, therefore, students were deprived of this educational opportunity.
About 30 minutes in, when Mulder is outside of Mr. Vincent's apartment listening to the gun fire within, it is extremely evident that Mulder's gun is missing its magazine.