sim engine play short much more often than it's told in the Gameplan, Or isn't 3rd down 25 yards counted as Long? :)
I have suspected this long time. To become sure, in some of my teams I put all three short plays to the bottom.
Exanple:
mfn27 week 11
Indianapolis 30 @ Jacksonville 30
I got 4 such short plays anyway. Even if the "bottom" is a few percent total, that's much more than a few percent.
(I haven't checked if some evil earlier owner :) have made mess in the Rules, but I have noticed this problem in other of my teams too, so it can't depend of that in all teams.)