Mine's the same way and it's not the body color seeping onto the suit, but rather corrosion originating from the zipper. I bought another suit from a local seller who had the suit removed on day one, only for him to take it out of inventory and have the same issue.
I can't speak for different climates but here in South East Asia a lot, if not all the HT MGS3 suits are breaking down, and you can buy a deteriorated Boss figure for as low as $40. All of my friends who own Snake and the Boss have some kind of deterioration of varying degree, hence I got rid of both of mine before they break down any further.
That, plus I hate them both anyway.