Most of the marks wash out - but a few are black and permanent. The other marks are soft brown spots that can be removed with a fingernail but if not dry to a brown spot that will wash out next time.
I have cleaned around the door seal and my cloth shows black marks. When I emptied the machine via the drain plug at the bottom the water was cloudy with lots of loose brown bits (some crumb size) in it.
No - the seal is stained black and there is no gunge.