I don't know if it happened to anyone else, but grabbing the second instrument after the boss causes the game to softlock, with Link showing it to the player and the sfx repeating. You can unsoftlock yourself by exiting, it saves that you beat the boss, but you can't grab the instrument and progress. Any help would be appreciated.

Known issue, only thing you can do is try exiting the game and grabbing it again.  Sadly we can't tell if the devs will fix this or not  in the future.