I have not loaded or looked at your capx,but if your score is still going up,You must have a condition similar to:-
>every 1 second...add 1 to score
so all you need to do is add
>player sprite is on screen
every 1 second ....add 1 to score
so when your square is not on screen your score should stop rising...
hope that helps.
As long as I can move left, right and fire, I'm Happy...