I've had this problem on and off for a long time. I completely reinstalled windows right before Endwalker and didn't install the gamepass app specifically because of it. So now I'm paying for gamepass on PC and not using it because I want to be able to play FFXIV. Although, I have still noticed it happen a few times, but it hasn't been nearly as bad. Before it was like every 30 seconds my controller would get stuck for like two seconds and the game was barely playable. Now it almost never happens and doesn't hang as long when it does.

I use a wired Xbox controller on PC. I don't think the type of controller matters, it's just the way the game responds to the device manager refreshing.