Except for maybe the top 3-4 defenses, every defense in the country has flaws, many of them serious flaws. The bottom line is the defense has been hung out to dry by the offense and has actually done a good job of keeping points down - the only stat that matters.
ND's defense has held every team but one to below their season-average yards per play (the one exception by 0.2 ypp) and every team below their season average. Three teams scored their season-low against the defense.