To ignore an app:

1. Focus the app that you want to ignore (make a window from that app frontmost).
2. Open the Rectangle menu and select "Ignore "
   

To un-ignore an app that you have selected to ignore, simply bring that app frontmost again, open the Rectangle menu, and deselect "Ignore "

Ignoring an app means that when the app is frontmost, keyboard shortcuts are un-registered from macOS. When the app is no longer frontmost, keyboard shortcuts are re-registered with macOS.