I would imagine that this is black marker, or she absorbed some stains from a pen.
G3s, as I've seen, don't particularly react to acetone nor magic erasers (unless on the symbol) so those should be safe to try to get rid of this stuff.
But
It's not surprising that neither of those will work if it is indeed ink or marker pens.
If it is, the only choice would be a sun fade. You can cover up the entire rest of the pony with a paper towel, then cover that with tinfoil leaving only the marker parts exposed and put her in the sunniest spot you can find. It could take like months though...to get that out. Or not, it depends on how strong the ink is. Because she is orange, you're probably pretty safe in doing that, because orange is pretty resistant to the sun (unlike green or blue which can lighten the skin/look bad)
Good luck for Scootaloo!