To my knowledge I've done nothing wrong. Randomly while going around to cleanse all the stones NPCs and guards just became aggressive. Now when trying to do The Path of Knowledge where I have to talk to Neloth, well I can't because he attacks me for no reason. I cannot revert to a previous save, so looks like I'll just play on one of my other characters.

Anyone else have this happen?

It happened to me when I first downloaded Dawnguard, what I did to fix it was to pay off a random 5 gold bounty in one of the holds. Try doing that and see if it works.

Yes I have all the skaal npc attacking me for no reason and cannot finish the main quest due to this. I'm going to attempt leaving the island and return to skyrim then travel back to solstheim to see if that fixes the issue.

I've just done this and it fixed it for me or leaving the island and returning may fix it, but op try both just to be sure.