Karimmaggio: 1) I don't think it's normal. I use a very inexpensive round rubber mute and a heavy rubber practice mute on my cello. It's never happened to me, and I've never heard of it happening to anyone else. No one in the orchestra I played in for three years as an adult ever mentioned it, and no one in the school orchestras I played in ever mentioned it. None of my three cello teachers ever mentioned it. None of the cello students I went to college with as an undergraduate or as a graduate student ever mentioned it. I use the practice mute nearly every time I practice. 2) I don't know how to remove the stain.
Sam's Music: My impression is that rubber mutes are rubber mutes are rubber mutes. They're all inexpensive, and none of them normally leave marks.