I was in the middle of playing through the creeper mines, when I paused it to put it into dock mode. It took about 5 minutes to put it into the dock (I had to walk down the stairs, etc, not a game problem), and it was in there for about 30 seconds, before I noticed that the (now undocked) JoyCons didn't work in the game. I could still use them on the switch interface, like the home button, but in-game, nothing happened. Even after re-docking, nothing worked. Was pretty annoying, as I had to replay the entire section.