Ive had a similar issue a while ago, but it was a regular pre 50 dungeon, not CT.

I was doing the stone vigil for the first time, and in the middle of the second boss, I was 90ked. Logged back in, and I was still grouped in the people I PFed.
I was still pretty new then, So I didnt know what to make of it then. Thought it was normal, when you got booted from the game while in the middle of an instance....:I

Anyone know what's going on with this?