What do green spots on the inside of a butternut squash indicate?
I always go with my gut in these situations, so scraping it off is probably a good idea.

If the green was not really dark and moldy looking, or really soft in comparison to the rest of the flesh, it could be that it just wasn't fully ripe yet in that area.  

Either way, you're planning on cooking the squash, correct?  I believe that this would be perfectly safe to eat now that the questionable parts have been removed.  I'd eat it with no qualms.

If the rest of the squash was firm, and not bad looking on the outside or inside, then I am guessing this is not a problem, unless said green part was much softer than the rest of the squash.