I had a Markarth Guard following myself and another follower in the Nchand-Zel ruins, and we got in a big fight with a bunch of falmer's, the Markarth Guard got in the way, adn I accidently hit and kiled him with an arrow...it then told me I had gained a bounty in The Reach...

How would I have a bounty when nobody other than some Falmer's who I then killed saw this happen, and we were deep underground where nobody else was traveling??

Doesn't make much sense...there is no way anyone whould assume I had any part in thei guard's death, let alone prove that I actually killed him...

I dont think this would be mod related... You may want to request this moved to the Skyrim General section.