Thank you all for your replies. I didn't even know substrate staining was possible from anything other than newspaper, so that was interesting to learn! I checked on her again this morning and tried gently wiping off the black marks as advised. They were pretty stubborn, but a flake of the black stuff (not her scale) stuck to my finger. The marks also look very superficial, so I'd agree with you all that it was most likely staining from her hide or something else in the enclosure. As for her chin smudge, I compared how it looks now to the photo I posted earlier and some of it looks like it came off on its own, but there's still a visible brown stripe there.
If it is substrate staining and such, then I think my best bet is to wait for her next shed.
Thanks again to everyone who helped me out!
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