Close the manual feed tray on the side of the printer if you are not using it. As long as you have paper loaded in the manual feed tray the printer will assume you intend to print from it and pull its paper.
Either that or you configure your manual feed tray away from the default any size/any type configuration. Pick a normal paper size and paper type that is either identical or unique to your other trays (pending on how you want it to behave) and then the printer will start responding the way you want it to.