You only score the contracts at the end of the game. When you score, you can choose whichever cards you qualify for but each building/track/resource can be used to score once.
Ah I should of clarified...I understand that you score them all at the end. The first couple times I played the game though, when it came to final scoring I thought that you HAD to score in a specific order.
The order is listed as:
So the first few times I played I thought that if you had an "Excavate" card you had to place your rubble on there and that you couldn't "save" it to use on a different card. So it sounds like I was making the game unnecessarily hard on myself. Does add a nice twist, which I kind of enjoyed haha