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Subsequently, one may also ask, why do I hear scratching in my ceiling?
There are only two options as to what the source of the scratching noises can be. It's either a critter in your walls or ceiling or something related to the building itself. It could be a loose pipe, a dislodged soffit panel or a piece of siding, or even faulty electrical components.
Consequently, what do you do if you hear mice in the ceiling?
Use fragrant baits such as bacon or peanut butter to attract foraging mice in the ceiling, and shift traps to new locations every four days. Permanently repair water damage along eaves by replacing the damaged wood and solving the drainage problem. Mice chew through rotted wood easily.
Most likely the cause of the noise is expansion and contraction of the material used for the new roof. In your case it sounds as if the roofer may have done some modification to the structure that required cutting into the roof. You might ask why would new wood on an old building make noise. Moisture is the answer.