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More than likely, your cleaning it "revealed" spots that were already there. You did not cause them.

There are other methods, such as Jimmy advised, but this is a barber hone & an heirloom,,, plus by looking at the photo, upper right corner,,, this hone may be starting to break down in the binder...

I'd let it sit in a bowl of Simple Green for a while, then remove & use a toothbrush to scrub it.
Then see what it looks like.

If no Simple green available,,, then a bowl of lemon dish soap.