I just finished up the quest rescuing Serana, and I returned to Fort Dawnguard (not as a vampire lord), and everyone was fighting, Isram attacked me, and had some weird thing going on around him. Is this part of the quest? I was sure so I reloaded a previous save and went to do a couple of other things. Any help?

yep its a quest

I know. The first time I did it the dawnguard were attacking me too. Must have accidentally friendly fire or something. Anyways, fixed the second time.