I have an Eastwood high speed buffer and get these black marks pretty often. They clean right off with a rag when the part is still warm or with glass cleaner if the part is cool. It happens more often when:

1) I've waited too long to apply more compound (white rouge)

2) The wheel needs cleaning. Eastwood sells a nice rake for cleaning the wheel.

Buff Rake

And yes, buffing machine much more effective than Mothers on dull or oxidized parts. But beware, buffing will produce chrome-like finish where Mothers will give you a more satiny finish on an already clean part. Sometimes one more desired than the other.

Mothers also good for final step when hand sanding/polishing a part not safe to do with buffer... Think crank spider.

Have fun!