I had just been sent on the quest to obtain the horn for the graybeards and after finding the note decided to stop in Whiterun before I went on to Riverwood so that I could buy the house for 5000 gold. All though the town I had no problems but once I entered the keep and started walking towards the throne my warrior girl that I had told to stay in town was attacked by Irileth for no reason and then I was attacked. Loading an earlier save file did not fix the issue. If I wait for the patch will this problem be fixed or will I have to load a save from two days earlier? I also tried sheathing my weapon to surrender, wouldn't work.

I think it is an Irileth bug. I would say part ways and go from there.