Near the end, Mulder jumps inside a buried metal box car yet still manages to use his mobile phone once inside.
When Scully finishes talking to Josephine Doane and turns to leave, you can see the reflection of the boom mic in the glass covering the photos above the window.
In the episode just prior to this one (Our Town (1995)), Mulder knows of the Anasazi, since he mentions them when talking about cannibalism, which is the prevailing theory about how they were wiped out. Yet, he reacts to the old man's mention of them as if learning for the first time, and is all too willing to accept aliens returning to their home planet as an alternate explanation.