Actually, you may want to turn auto-upgrade off in Settings on the Wayfarer website. When the toggle is on, it applies upgrades automatically for you. I keep it turned off, as not all I submit needs an upgrade.
Unfortunately, once an upgrade has been applied, it can’t be given back, nor can one gain an extra submission. Extra submissions in general are being asked for by many, as some do use up their 40 nominations per game per day limit.