Strange, I did the exact same thing during ACT 1 and had no issues with the Owlbear Cub. More precisely I had Animal Speaking active, persuaded her that I am no threat, got too close, killed her, spared the cub.
So could be just a random bug or triggered by something else, because even when I left her alive she would later be killed by goblins and the cub had no issues being in the gobo camp.