From what I have seen, this is just me, they come about from water/liquid exposure, from rubbing, and the most common: stickers. Many Archies were resold, but thought to be the pond scum of comics and were never bagged, never boarded, and sold with a sticker directly on the comic.
It is not limited to the red ink covers either since I have seen the same effect on green blue or yellow covers. It must have been the ink they used? Not 100% sure there.
As for your copy, I suspect it had a droplet of water/liquid fall on the cover which was wiped off. Could also be rubbing.
I don't have my books with or I'd show you multiple examples.