I picked up a used SG 2000 (2006 model) recently and the large leather honing wheel has a two gouges that to me seem pretty substantial. They don't run the entire width of the wheel, but are deep and wide enough (2-3 mm) that there is no possibility of smoothing them out. I'm guessing maybe previous owner caught the edge of a blade accidentally at some point.
Is this a common or harmful situation?
As long as your tools are wider than the cut and flat, it shouldn't be an issue. It'll be awkward if you try and do carving or turning tools or narrow chisels.
Replacements are available from http://www.tormekstore.com Click the link for "Repair Parts".