Catalina stacks icon overlapping with files

I wanted to figure out how to turn a folder into a traditional mac application, and I heard that when I put the correct files in the correct folder system and changed the parent folder's file extension to .app it would automatically turn into an application. I did this and it worked perfectly, but it messed up my desktop. I have stacks on always, but for whatever reason folders are never included in stacks. My folders have always been listed individually and there has never been a button or whatever it is to collapse the folders into a stack. I assumed this was supposed to happen, though. I unfortunately don't have a screenshot of my desktop before the .app change, but here's what it looks like currently:

Behind the folder in the bottom right corner is another 'Folders' stacks icon thing. I have tried clicking on the icons, adding/deleting folders, disabling/reenabling stacks, adding/removing/switching desktops. Edit- restarting the computer works but I want to be able to do this often so is there a faster solution?

Thanks! 😊