Coaching Staff, Colin Kaepernick Continue to Hold Back San Francisco 49ers

It started out easy enough for Colin Kaepernick and his San Francisco 49ers offense. Starting hasn’t been the problem, with touchdowns on their opening drive in three straight games.

No, finishing is still the problem. Which has made winning a problem, the latest stumbling disappointment a 23-14 loss to the Arizona Cardinals.

Quickly, as we already rumble towards the quarter pole of this 2014 season, San Francisco fans are thrusting the burden of blame throughout the 49ers’ sideline, with few spared. That includes Kaepernick, offensive coordinator Greg Roman and head coach Jim Harbaugh.

Another second-half demise came Sunday afternoon in Arizona during a divisional clash against an offense without its top quarterback and a Cardinals defense that will play the rest of 2014 without pass-rushers who were responsible for 21 of their 47 sacks last year (the latest loss is John Abraham). A wicked injury spell continued when the Cardinals also played nearly half of Sunday’s game without cornerback Antonio Cromartie, who suffered a knee injury in the third quarter.

Yet still the result was a divisional loss, followed by more confusion.

How is it that a team which added Stevie Johnson in the offseason, traded up for Carlos Hyde, and secured Alex Boone following a bitter holdout can sputter this much to start a season? Answers need to be found fast with the Philadelphia Eagles and Chip Kelly's circus offense coming to town next weekend.

Already through three games the 49ers are halfway to last season’s loss total. Throughout the Harbaugh era San Francisco has lost only 11 regular-season games over three years, and they’ve never dropped more than four in a single season.

What’s troubling is the way that losing is happening, with strong starts ultimately giving way to poor, penalty-marred play down the stretch. The 49ers have entered the locker room at halftime leading by more than a touchdown in each of their last two games. They led 14-6 against the Cardinals and 17-7 in a Week 2 loss to the Chicago Bears.

The combined second-half score in those games: 38-3 (and 53-3 when we toss in Week 1 and the Cowboys’ second-half scoring). That’s right, the 49ers have scored three points in the second half this year.

	Points	Offensive Yards
First Half	59	590
Second Half	3	405

The anemic second-half offense is compounded by the defense giving up 21 points to the Bears in the fourth quarter, and handing the Cardinals free field position through backbreaking penalties. The latter problem isn’t a new one, but Sunday the lack of discipline became even more glaring.

Every opportunity to score was crucial in a game that was decided by only nine points. But there the Niners were, getting docked over 100 yards in penalties for the second straight week.

	Penalties	Yardage
Week 2 vs. Bears	18	118
Week 3 @ Cardinals	9	107
Total	27	225
Combined Total for opponents	15	94

For the faithful sitting at home there’s an instinctive, almost primal reaction to scream about biased officiating when their team is penalized heavily. But although it’s frustrating, grey areas in football officiating will always exist due to the sheer pace and chaos of every snap. Accumulating 225 yards in penalties over a two-game stretch—more than enough to cover the field twice—speaks to something far larger than a petty zebra conspiracy.

It speaks to a lack of discipline, which begins with the head coach. Discipline is a core Harbaugh value—one which a veteran standout under his charge completely abandoned.

In the third quarter Sunday, Anquan Boldin caught a pass that would have put the 49ers in a goal-to-go situation, fighting for extra yardages in the middle of the field before being brought down at the Cardinals’ six yard-line. But then he shoved and butted heads with Arizona safety Tony Jefferson, evidently out of a need to establish some Alpha-male dominance, forgetting that scoreboard dominance is the only kind that matters.

A 15-yard unnecessary roughness penalty erased the goal-to-go situation. Then a clipping call on Jonathan Martin moved the offense back further. Over four plays the Niners went backwards 30 yards, and a field-goal attempt was then from a greater distance (45 yards), meaning a lower-than-usual trajectory was needed. This meant the kick was more susceptible to being blocked.

Which is exactly what happened. An opportunity for seven points became hoping for three...and then zero. And it all started with Boldin’s moment of petulance.

After the game Boldin expressed frustration over the refereeing. But he took responsibility for his penalty.

Per a report by San Jose Mercury News beat writer Cam Inman, Boldin acknowledged, “My penalty is my penalty. I shouldn’t have done it,” Boldin said. “Guys were taking shots at me all game. I told coach that. I told the refs that three times.”

The truly creative approach to game squandering through penalties came before that. On back-to-back plays the 49ers were dinged for unnecessary roughness because of hits on Drew Stanton. One from linebacker Dan Skuta, who hit a scrambling Stanton late after he had started his slide.

In fairness to Skuta, the play was difficult and so was the call. Stanton started his slide late, and Skuta was already launching to stop the scrambling quarterback (the hard way).

But the reality of today's NFL (one you're welcome to hate) is that officials will always favor the quarterback, especially after his head ping-ponged off the turf.

Then Patrick Willis went high on Stanton, another standard modern NFL flag. Two plays, and 30 free yards. The Cardinals moved from their own 38-yard line to San Francisco’s 25, eventually setting up what would be the game-winning touchdown on a 21-yard pass to John Brown.

The game was never out of hand, though, so there was no reason for desperation. Nor was their really any cause to depart from running the ball—the 49ers’ offensive motor. But there was Greg Roman, giving the ball to Frank Gore only once in the second half, and running only twice. Twice. And in total Gore and Carlos Hyde combined for only 23 rushing yards on nine carries (3.4 yards per carry).

With tight end Vernon Davis out, a key piece of the San Francisco passing game was missing Sunday, but the 49ers offense still has plenty of weaponry. So asking Kaepernick, who often makes bad decisions, to do it all with his arm and with his legs on designed runs isn't an effective way to get a lead, or keep one. Giving nine carries to running backs is absurd for an offense that averaged 31.6 rushing attempts per game last year.

The 49ers we saw in Week 3 weren't the 49ers we've known for the past three seasons. They weren't the Harbaugh-coached team we know, nor was Roman's unit the offense that we know.

It was all very unfamiliar territory. The season is young, but in the NFL it always gets late early.