Well, the "liked" is sort of my interpretation, but Brian mentioned that Joss basically said, "Don't bring Cordelia back," and then Brian did it anyway. Granted, he didn't "bring her back" as in resurrect her, but she does make a pretty significant appearance, which seemed to be contradictory to what Joss wanted. (He thought her exit was big and complete, and there wasn't a further story to tell with her.)

I highly doubt that Joss would come out and say he disagreed with anything Brian did in ATF, though. If he didn't like it, he'd probably just stew quietly (and maybe refuse to work with him on the Spike series).