The Science of Illusion - S1-E20
Visible crew/equipment: After Britta accidentally bumps the gurney into the window, she grabs the body bag in a failed attempt to keep the corpse from falling out into the quad. Right as she grabs the body bag, look on the ground behind her. Someone slides a mat in behind her for her to fall onto. (00:13:50)
Aerodynamics of Gender - S2-E7
Visible crew/equipment: When Pierce's drone is following Jeff and Troy, as the two go through the bushes, you can see the string the drone is attached to as it "hovers."
Intermediate Documentary Filmmaking - S2-E16
Visible crew/equipment: When Jeff runs to the car which his father drives and opens the door of the driver, you can see the camera in the side window of the car. You can see it's a set camera and not a 'handheld type', the one that Abed is using during this episode.
Biology 101 - S3-E1
Visible crew/equipment: At the beginning of the episode, after Pierce rejoins the group and Jeff and the others begin to leave the room, watch Britta as she stands up. When she turns away from the camera, you can see the actress' microphone-pack in the back of her jeans briefly. (It's hard to spot but it's there, and is confirmed in the commentary track.).
Basic Crisis Room Decorum - S6-E3
Visible crew/equipment: While Chang is reading the message about the attack ad, you can see a very visible camera used to film Winger.
Answer: His attempt to "kill" Jeff was to roll at him as an iPad on a stick. He knew it wouldn't work, but it played to the story that he was a killer as he knew Jeff would tell people about it, or attempt to retaliate for it.