Mulder pulls a refrigerated truck up to a warehouse in Washington D.C., yet Scully later on (around 34:40) states that the warehouse is "just outside Washington D.C. in Sethburg, VA."
Mulder tells Scully to meet him at "The Smithsonian." This is a useless direction because The Smithsonian Institute is actually a series of locations - 19 museums, 9 research centers, and the National Zoo, to be exact - not just one museum or building. She could not know where because Mulder did not specify one museum or building, and they aren't all in the same place; there are several on the Mall, but not all of them are there. The screen also says that they are at "The Smithsonian."
During the alien autopsy, they are wearing little more than home decorating dust masks. Something far more substantial would be expected if not full biological isolation garments.