Pennsylvania sheriff departments do not perform routine patrols or criminal investigation since they are "servants of the court." As a Commonwealth, most PA municipalities provide their own police force. If the municipality chooses not to have their own department, the Pennsylvania State Police are tasked with coverage. In addition, the PA State Police also serve as the "highway patrol" quoted by Scully towards the end. The Pennsylvania Highway Patrol was absorbed by the PA State Police in 1932.
(at around 14 mins) Deputy Pastor's voice is heard saying "I've seen them fire muskets before." However, his mouth is saying something else.
The Peacock family have lived in Pennsylvania since the Civil War, yet are depicted as stereotypical inbred rednecks who speak in Southern dialect. One of them makes a disparaging comment about the "War of Northern Aggression," a Confederatism which a Pennsylvanian would be highly unlikely to use. This and other elements, including a running gag based on The Andy Griffith Show (1960), appear to indicate that the story was originally intended to take place in North Carolina.
Mulder and Scully do a terrible job of clearing the house. They miss areas, such as under beds and in closets, where people could be hiding, and they seem to entirely bypass the room with the mother under the bed.