I have a 4 month old Honda Forza 125 bought from new. I cover it after every time I use it.

Take it back for a warranty check as the color could be rust stain
it should be covered by warranty at 4 months
there could even be a service notice from honda on the subject
one point
do not use washing up liquid on metal paint work as it contains acids and alkalines that create a problem for the finish
use proper car wash

Some propriety vehicle covers are made from a woven synthetic material that will move about through the action of the wind and very efficiently remove paint.

I heard of a caravan being covered with one of these for the winter and when the cover was removed a few months later a considerable amount of paint had been removed leaving areas of polished aluminium.

Such covers are marketed as all-weather protection but they really should not be used outdoors, especially considering bike components do not have a generous paint covering in the first place due to the danger of the finish cracking or crazing and the increased ease that chips and scratches can be inflicted on a bike. A thick coating of paint is more susceptible to damage.

I suggest you thoroughly read the literature supplied with the cover and if appropriate contact the retailer in the first instance. Your contract is with the retailer and not the manufacturer and meanwhile obtain two or three estimates for repainting the damaged areas.

If all else fails Honda could be approached. It is also possible your vehicle insurance would pay for repainting.

Good luck!