I should add, I have no bounty that I'm aware of, and even using the same spell to calm the Falskaar guards and pay off a bounty it gave me upon casting the spell, they immedietly became hostile again as soon as the dialogue ended.

are you a vamp cause thats another way for guards to go hostile on you

Nope. Played through Dawnguard on the Dawnguard side, and when asked for Soul Cairn I chose Serana to soul trap me.

Also my disease resistance is at 100% so I shouldn't be able to contract it, and even then I frequently check for diseases.

Did you ever find out what was going on? Just had this glitch happen to me as well. Not sure what triggered it or how to fix it.

Oh god it's been a while.
I could be wrong but I "think" I couldn't actually stop it and worked around it by using a Mass Calm spell and defeating the enemies then it progressed as normal.

If you've not got enough magicka to cast it, you can try "tgm" in the console (toggle god mode) which lets you cast any spell (that you've know of course) without requiring/losing that mana.

Knowing me I might have just used the console to directly click and kill each enemy. It's been a while so I don't have perfect memory on what I did.

I know they say not to use the Command Console for this sort of stuff but...Well when it's your only option, it's your only option.

Thanks for the reply! :D I wasn't sure I'd get one, seeing as how long ago you posted this. Thanks for the advice too, I'll give it a go. Fingers crossed it works. Very grateful!

I am having the same thing happen to me. Not sure how to proceed, but will try what you did.

heya I'm late to the party but if the issue is that you randomly got a bounty, you can instantly pay off your bounty and be teleported to the Amber Creek barracks! (Maybe kill the enemies first though) It's what I did! I targeted one of the npcs and wrote the command:
paycrimegold 40
it fixed it

It wasn't bounty related.

A very late replay and possible reason...for me at least the reason was that I earlier inside the fort gave Jarla and the kid their own weapon instead of letting them pick up whatever they find on their own.
As soon as I removed the weapons I gave them, they picked up something from dead bodies and allied attacks no longer happened.

Cheers!

Paycrimegold 40 worked for me. Still had the problem of random 40 bounty hitting me when I got close to npc combat.