Just to be clear, the controller still has functionality. I can still inspect, drop and use items with the dpad, and open the map with select (think it's the share button with ps4 controller). Problem is, whenever I press any of those buttons It ALSO causes the bottom crafting tab to glitch and I get the annoying rapid clicking sound. It's like the game thinks the crafting menu is still open and is trying to do something with it, but it cant. This is very annoying because I use the dpad a lot while playing. I think this problem has something to do with a recent update. I cant find anyone else who's ever experienced this issue. Sorry if it's still not clear. It's just such a strange thing to start happening all of a sudden.
Update: After a bit of playing around, the problem goes away when I open my inventory by pressing RT, but comes back after opening the crafting menu again (LT). If I want to keep interacting with the items in my inventory, using the dpad, without the tab glitch/annoying sound, I have to keep pressing the open inventory button. Not ideal.
Here is a picture of the other issue with the settings overlapping: