I have no stains on my mat -- I scrub out fresh stains with Mothers Carpet Upholstery cleaner (works extremely well) and then top it off with Meguiar's Carpet Deodorizer.
I do have what seems like an indent of where my heel would be on the carpet by the pedals. No scrubbing, washing, or vacuuming seems to fix it. Could very well be the dress shoes. I can't see indents like that coming from sneakers or driving shoes.