Just clean them off with the above mentioned rubber roof cleaner and if you want put a coating of uv ultra violet protectant on.
Rv rubber roof black spots.
How to clean mold from an rv roof.
I believe you may be seeing the bottom ply and not all the way through the membrane.
The rubber roofing membrane consists of a couple plies or layers.
If the roof of your recreational vehicle is made of rubber then you may realize how frustrating the situation is.
Owning and staying in an rv can make you realize that one of the bad things that might happen to it is its roof being filled up by molds and horrible black spots.
For those with fiberglass roofs this can be cleaned away in exactly the same way as mold spots on the siding are cleaned.
However if you have a rubber roof the job becomes a bit complicated.
Occasionally campers will have issues with mold growing in their rv roof.
Wondering how to kill mold on your rubber.