More than likely you were playing Destiny while the weekly reset occured. Because of this the nightfall becomes available, but since you were already in a previous session it doesn't reset the rewards for the new week. You need to close the Destiny application/dashboard before attempting the new missions or you will not be rewarded.
Luckily you can still get your reward by playing through the mission a second time, just be sure to log off and back in next time.
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Edited by Eb0La FeveR: 1/20/2015 11:16:01 AMUgh, that sucks.