I think the fix for An untimely end messed up my decision?

[Brandon Navarro]

I could be wrong because I had no idea this was a bug and was able to decide to let the assassin live while playing last night. However, while playing today, I was finishing up the last of the side stuff in dawnshore when I randomly teleported to the gate and went straight into the encounter with the rebel who gave me the warning. Kai made the comment that maybe we shouldn't have killed Ygwful???? Right after that encounter it teleported me to a camp and went into a cut scene with Kai and Marius where we had to convince Marius to travel to the Emerald Stair with us. All of this happened while I was in the middle of grabbing the last treasure map item in Dawnshore?  

I am pretty salty since I was trying to be a good guy Geralt on this playthrough. 
Anyone else ran into this issue??