So I was in vampie lord form killing people in windhelm and I killed this one guy and It came up as I killed a theives guild contact or some thing like that and I had to pay restitution to the guild. My problem is how did they know it was me in vamp form?

ehmm not for be unpleasant but this thread is usless cause its' simple, i think the system recognizes you and then u need to pay (or maybe it's just a bug, correct me if i'm wrong)

It's always been that way. I attacked a fence in werewolf form and I had the same thing happen. VL is no different. Just like if you murder a bunch of people in a town, when you come back their family members or any surviving witnesses will call you degrading names and disrespect you as if they know it was you who killed so-and-so. I believe the game has a separate background calculation different from the one for bounty and guard reaction that applies to NPCs and guilds, specifically.

Basically, be careful to avoid breaking any guild rules in ANY form you are in, since you're responsible no matter what. You're still conscious of what you're doing, even in Beast Form, so think of it that way. My method is to use the Howl of Terror and run away if I run into an NPC that I need left alive, and as for guild members, I just avoid all of them.

NOTE: Interestingly, there appear to be some factions that don't regard your werewolf form as a threat (aside from the Circle of the Companions, obviously). Still not sure about that for the VL, aside from the vampires in Castle Volkihar, obviously. I found this out when I went to Largashbur with my Orc werewolf in Beast Form. They just went about their business and talked to me. Mostly they commented about how I should put clothes on, lol. But I just waited for almost 20 hours to change back in the longhouse and they paid me no heed otherwise. I think this may be because of the quest for Malacath, or the fact that I'm an Orc.