I think the stains are getting on my prints once in awhile. They really shouldn't touch the bottom of the tray enough to pick up a stain, but once in awhile I think it does. My tongs also get stained from rubbing the bottom of the tray, and they transfer to the prints I think.
Now that I think of it, I don't think I had the staining problem until I started leaving the developer in the tray overnight with plastic wrap over. Now I pour it into a small container in between sessions (if is is still fresh that is).