This is where you learn the benefit of masking off the fretboard with tape before working on the edges of the frets!
You can also buy thin stainless steel fretboard protectors to use when working on frets to save the fretboard getting marked. These are the ones I use: http://www.chrisalsopguitar.co.uk/sh...ard-protectors . StewMac also do them, but call them 'fingerboard guards'.
I know it's something else to buy, and the cost all adds up, but they are something I use a lot - especially when I decide its time for a guitar to have its frets polished again and I work up through the Micromesh grades and finish off with some metal polish.