I usually calculate my points in advance (right after they're posted on the tdf site) and I think I might be missing some 5 points. Sagan, Boasson Hagen and Cancellara might have received slightly less points than they deserved. Here go the calculations:
Sagan got 51 points but he should have gotten 53 (35 for the stage win + 8 for his 8th place at the intermediate sprint + 5 points for having the green jersey + 3 points for being third in the KOM classification + 2 points for being the fourth youngster = 53 points)
Boasson Hagen got 40 points, but should have gotten 42 (30 for being second on the stage + 6 for being 5th on GC + 2 for being fourth on the green jersey classification + 4 for being second in the young riders competition = 42 points)
Cancellara got 35 points but should have gotten 36 (22 for 4th place on the stage + 10 for yellow jersey + 4 for being second in the points competition = 36).
I know, 5 points is not much, but might prove useful at some point... Could you please check it out? I might even get up to 13th in the overall yearly classification