It's possible that when Halsin turned into a mouse he ran through flames/other AoE and died. That's what happened on one of my playthroughs. In this case the game thinks he's freed (because you did successfully free him) but at the same time he's dead.
Honestly you're probably screwed unless you wanted to load an earlier save. I'd compile all the relevant info you can think of and send a bug report to Larian using their bug reporter.
Initiate the grove battle and Halsin's quest should update maybe? (and by update I mean probably say that he died)
