Why Did the Patriots Struggle in Short Yardage Situations?

Teams are converting short yardage plays at at a 63.6% conversion rate. They are converting rushing attempts at a 10% high clip than passing attempts (67.4% vs 57.6%).

So why did the Patriots draw up just three rushing plays in their nine short yardage situations (not including a Tom Brady scramble)? Why did they call four passing plays on their five downs inside the Chargers 5 yard line?

Why were they just bad in short yardage situations?

If teams are converting rushing plays at a 10% higher rate, why are the Patriots drafting drive killing play sets in the most important area of the field? And that's not to say the Patriots should hand the ball to LeGarrette Blount, even though he converted on two of his three short yardage rushing attempts.

@MikeClayNFL Here's my numbers since he entered the league, min 50 attempts since Blount entered the league in 2010 pic.twitter.com/Wu4JttVaAZ

— Rich Hill (@PP_Rich_Hill) December 7, 2014

If your team is taking two snaps from the goal line and one of them isn't a Tom Brady sneak, you're calling the wrong plays. Also, with Jonas Gray converting 7/9 attempts, perhaps he deserves some snaps in short yardage plays?

There always seems to be an element of overthinking the play with Josh McDaniels and it's something that he needs to master as the regular season finishes. If Tom Brady is 8/40 (20%) on passes 20+ yards down the field, why have we seen three deep shots on 3rd and <2 this year (one was picked by the Colts, one was against the Dolphins, and one was against the Vikings)?

It's one thing to pass the ball on 2nd and short, because that's gamesmanship; the defense has no idea what's coming and offenses should have the ability to catch the opposition off guard. But to throw two consecutive passes (which the Patriots did on the goal line against the Chargers, and had done against the Raiders on the goal line)? That's overthinking it.

It should be noted that the Patriots have passed on both 2nd and 3rd and short five times this season with two conversions, which isn't too far from the 56.8% short-yard conversion rate that the Patriots boast on the year. But it's a sign that the Patriots aren't trusting their running game as much as they should be. The Patriots need to start calling smarter plays in the short yardage situation.