A Thing About Machines - S2-E4
Visible crew/equipment: When Finchley is being chased by his "driverless" car, you can see the driver crouching down at the wheel.
Visible crew/equipment: An equipment shadow moves across the back of Ellington's coat as Brother Jerome is telling him how the Devil was captured. (00:14:30)
The Lateness of the Hour - S2-E8
Visible crew/equipment: As Robert is pouring Dr. Loren's drink, an equipment shadow moves across the top of Jana's head in the foreground. (00:08:20)
The Lateness of the Hour - S2-E8
Visible crew/equipment: The boom shadow intrudes briefly at the upper left of the shot as Jana stands at the window and says, "Rest in peace." (00:16:15)
The Lateness of the Hour - S2-E8
Visible crew/equipment: When Jana is screaming "No pain!" at the top of the stairs, a film crew member's shadow can be seen moving on the wall behind her. (00:22:30)
The Trouble with Templeton - S2-E9
Visible crew/equipment: When Booth walks over to Laura and Barney at the speakeasy, the moving boom mic casts a shadow on the wood pillar behind Laura, at the top left side of the screen.
Visible crew/equipment: When Sykes opens the Sheriff's office door to leave, the "sky" outside has a very large equipment shadow on it, hanging over the building across the street. (00:05:10)
Mr. Dingle, the Strong - S2-E19
Visible crew/equipment: In the scene where Dingle is waking up to the alarm clock, you can see a camera shadow moving over the bed.
Visible crew/equipment: When Chris escorts Grandma Bayles up the stairs, a blocking mark is plainly visible at the lower right, chalked on the carpet. (00:05:25)
A Hundred Yards over the Rim - S2-E23
Visible crew/equipment: When Christian walks up to the man in front of the diner, you can see a crew member in a plaid shirt and white pants reflected in the man's sunglasses.
The Mind and the Matter - S2-E27
Visible crew/equipment: While Beechcroft talks to his boss in the men's room, the boom shadow moves across the wall at the upper right of the screen. (00:03:35)
Answer: It's explained in the episode. The aliens are experimenting to see how humans react to various scenarios. This just happens to involve them using super strength.
Thanks. It's been a long time since I saw the episode so I forgot.