It got water in there somehow. Maybe the cover itself has passed its useful life and water gets thru.
I cover my boat to keep it from getting mildew inside, and also to keep it from freezing and ruining the insides. Boats are not designed to be waterproof.
OTOH, my RV has a rubber roof that's intended to keep it dry inside. We have 2 RVs. The oldest is a 1964. Never put a cover on it yet.
BTW, we live in Buffalo, NY. Hardly anyone here covers their RVs. IMHO, covers do more damage than not covering.