Suggest you clean it off, and keep an eye on the mower before the next mowing. Are you the only one who uses it? If not, something about the way another person is using the mower may have some clues about the black marks.
If you are the only user, then watch and see what happens after you clean off the marks and put the mower away. Do the marks just appear on their own? Do they appear after you've fueled the mower? Do they appear after you've started the engine? Do they appear after you've mowed the lawn (or during)?
I'm pretty confident there's nothing about the mower itself that would cause black marks like that to simply appear, *unless* there's oil, fuel, or some other fluid leaking, but even then, I can't imagine what could leak that would cover so much area on the mower.
If still no solution, I'd take it to a dealer for a full inspection. They are experts, and can probably tell you exactly what is going on. If it's shown to be a genuine factory defect, and the mower is still under warranty, repairs are typically covered by Honda.
Hope this helps.