I had much the same happen with the regular Solitude guards, I had not started the CW quests but was... ahem... taking care of some business for another faction that got me in hot water with the Penitus Oculatus. I had to kill one of them, at which point another one of them spotted me and came running. Right behind him was a Solitude guard and when the guard raised his weapon I really thought he was coming after me as well, but he attacked the PO agent instead. I guess the guard didn't see me do what I did that made the PO guy attack me.
Later on I was back inside Solitude and literally walked right into two PO agents outside Castle Dour who attacked me on sight. The Solitude guards didn't like that either, lol.