correct preposition

It would depend on whether the damage is on the surface of the ceiling (like a water stain,) or in the ceiling (actually up inside the ceiling where you can't see.)

There is some damage to the ceiling. This covers all eventualities.

"In" the ceiling would be incorrect.

The ceiling is a lining between the room and the roof space or possibly attic. The ceiling is generally only a few millimeters thick.

Roof is the covering over a house but most Australians would use the word roof to indicate the covering and the space below it until intersected by the ceiling. Americans would call the roof space attic.