Yeah, there's definitely some bugs with this questline. But it's not a consistent thing.
First time I did it, I was able to talk to Karlach after killing Anders but it wouldn't update the Kill Anders quest no matter how many times I went through the dialog with her. And she remained where she was no matter how many times. But most of my other run-throughs, after talking to her the quest updates and she heads off to Baldur's Gate. On my most recent one I talked to her, and she left for BG, but the quest didn't update.
I haven't actually tried the path of killing Karlach. But this is the first I've seen where the wrong quest was updated.
