try calling the company or Gamestop. I had a similar issue with Emerald for GBA

dang during the update something probably went wrong I recommend calling the nintendo hotline at 1-800-255-3700

Based on research of the game's controls, it seems like you have a sticky L button on your 3ds (Quickly scroll through menus and pulling up the data for a move instead of executing it). I don't know what the PlayNav is but if you open whatever that is and you notice it keeps switching apps, that would also confirm this. Sometimes I get problems with sticky keys on my keyboard, and simply hitting the sticky key a few times does the trick. I'd recommend fidling around with L button gently to see if you can get rid of the stickiness, you may need to clean it, but if it's busted, you're looking at another 3ds, which if you just got it recently could very well be covered under a limited warranty.

Thing is the PokeNav doesn't switch over like it's stuck. Just the Menu and Fighting is the issues XP

EDIT: Ok I just tried the L Button. Apparently it was that :/
Thank you! :D Would have never thought of that one XP
HAha

Good! At least it wasn't something more catastrophic!

Now to draw Scout XD

But yeah thankfully ;w;