The Nintendo Switch and Modern Console UIs

[A Black Falcon]

So, I was just playing Spiral Splatter, and I switched over to the Gamecube controller because its analog stick is a lot better for this game than Switch controller or Joycon analog sticks are, particularly because of the 8-angle well instead of the Switch's circular one. When I wanted to stop playing and go back to the system menu, however... I couldn't. The Joycons would not turn on to pair with the system no matter what, for what reason I have no idea. And since the GC controller doesn't have a Home button, I was stuck. I ended up having to UNPLUG my GC controller from the USB-to-GC-ports adapter, which is insane! The only other option would be removing the Joycons from their holder things (I have them in those battery-holder things since it adds some nice size to the Joycons, making them as thick as a Wiimote; much better for holding!) and put them into the system and remove it from the dock; I presume that would also have worked, but that'd be a pain. Of course having to go over there and unplug a controller just to turn a different controller on is a huge pain too, to say the least.

Is this a common issue, or am I just having issues with my Joycons? If it's the latter, this is not a problem any other Nintendo system has ever had, and I have no clue how they messed the Switch OS up so badly that Joycons won't pair while you're using a Pro Controller, but it's quite unacceptable. If it's still like this when Smash releases that sure will be nice...