Other parts of the paintings are exaggerated or abstracted. (The horse forms in particular.) It doesn’t seem unreasonable to believe other aspects might have been abstracted from or emphasized beyond literal reality.
With no evidence of spotted horses existing at that one it wasn’t a totally unreasonable speculation.
How can we tell if there were spotted horses 1000s of years ago except through pictures> I'd believe the pictures known to be of that age before I'd believe that there were none. What about humans? Do you think that there were blue eyed Neaderthals? Green eyed cats? Blue eyed wolves?