You must pour at least 4 fl. oz. (119 ml--a revi'it) of wine or other beverage into the havdala cup--this is halacha.  However, to symbolize that we are blessed (siman bracha) with wealth, overfill the cup (non-binding custom).

For havdala, pour at least a revi'it (4 fl. oz., or 119 ml) for enough wine (or other beverage being used) to overfill the cup. This is a non-binding custom, not a halacha.
Reason Doing so is a symbol of blessing (siman bracha) that we are so rich that the wine or other drink that we spill is not important. Don't overfill your cup if you are using wine from a shmita year!