I'm not a metallurgist, but I don't believe stainless steel actually rusts.
It does, however, pick up scrapings of non-stainless steels when you use your allen wrench on them, brush them with a steel wire brush, or expose them to the road salts and sand that covers the roads in snowy areas. These scrapings are what is likely rusting inside the allen cup.
Stainless steel will corrode - it pits in seawater, saltwater boaters have lots of experience with this.
If you have an old stainless steel cooking pot, you might see it there, too.