Not sure if this is a roofing question, because I don't believe it's a loose shingle and there's nothing that I can see from a distance that appears to be loose. The flapping noise is directly above the exhaust fan in the bathroom. It's only bothersome when it's windy. Does the exhaust fan vent on the roof have something inside it that is designed to perhaps flap to let the air out but keep the rain from coming in? And therefore it's just the nature of the design? Thanks

Teh flapping noise is the air baffle they install to prevent both birds from entering back into the fan housing or duct work. When the wind blows it causes the baffle to open and close. Nature of the design.

It sounds like it's probably just turkeys roosting on your roof.

On some exhaust fans the little flap is built into the housing in the ceiling just outboard of the fan, on others it can be part of the vent cap on the roof. In either case it should be fairly simple either to disable the flap by wedging it open or to pad the edges with some gorilla tape or something so it will flap quietly. If you disable it, recognize that you are basically opening a 4-6" hole in your ceiling so that heat and AC can escape and if there is no screen on the vent cap, insects, etc. can get in.