What you have sounds alot like what alot of my ponies had, its just rust from the washer. Somehow, I'm not entirely sure, it get all over the insides of the ponies. Gross but mostly harmless unless untreated.
This is what I've done for all my ponies that required cleaning, which are alot because I buy work lots! Find an old tooth brush or a small bottle brush (those are best because they bend to fit the legs and harder to each areas). Mix plain old liquid soap (if your worried maybe get the antibacterial kind) with Baking soda (yes) into a paste. Put some on the tooth brush and start scrubbing. The really nice thing about his is you don't have to worry about side effects so you can clean the entire pony with it, including the hair.
Unfortunatly it's nearly impossible to get all fo it off, most of mine still have stuff at the bottoms of the insides of their feet. So far I haven't had rerusting issues, but we'll see.