It's already been asked about on Q&A and the answer won't get more detailed than that.
This has been in the rule book the last three seasons(at least) and is always asked about in Q&A and is always the same. I've never seen a team get a penalty for marking a frisbee/gamepiece. I think the intent of the rule is to make sure all balls are always functional. Ie. 2013, teams that (occasionally and unintentionally) shredded frisbees slightly where okay, teams 2012 plenty of balls ended up marked with black streaks, and it was rarely an issue (in regards to penalites and such)