San Francisco 49ers: How Bad Are Their Penalty Problems?

The San Francisco 49ers lead the NFL in penalties in 2014.  They have been flagged 36 times or 12 per game, significantly higher than the second-most penalized team:

Team	Penalties	Yards	Declined	Offsetting	Total Flags
San Francisco	36	305	3	2	41
Pittsburgh	31	262	6	3	40
New England	30	322	5	1	36
Washington	28	299	3	5	36
Tennessee	28	244	2	1	31

This is obviously not good, and it has cost the 49ers big time in both of their losses this season in ways both large and small.  Four plays from the Arizona game sum up how the 49ers keep shooting themselves in the foot:

• On 3rd-and-10 from the San Francisco 37 in the first quarter, Justin Smith slides his way into the backfield and sacks Drew Stanton for a loss of four yards, setting up a probable punt.  However, Eric Reid is flagged for illegal contact on the play, giving the Cardinals a new set of downs.
• Later on that same drive, on another third-down play, Stanton hits John Brown for a gain just about at the sticks—it looks, upon replay, that it would have been just enough for a first down, but it’s close.  The need for a measurement is taken away, however, when Reid brings Brown down by his facemask, tacking 15 yards onto the play.
• In the third quarter, Drew Stanton scrambles for seven yards and then slides down at the Arizona 45-yard line.  As he’s sliding, Dan Skuta hits him with a shot and is flagged for unnecessary roughness, bringing the ball onto the 49ers’ side of the field.  The drive ends in a go-ahead touchdown for the Cardinals.
• At the beginning of the fourth quarter, the 49ers face a 3rd-and-8 from the Arizona 19-yard line.  Jonathan Martin is called for clipping, moving the ball back to the 34-yard line and causing the 49ers to attempt a long field goal, which is blocked.

USA TODAY Sports

You can argue whether or not some of those fouls were actually fouls, of course.  David Fucillio of SBNation highlighted two questionable hits on Drew Stanton, including the Skuta penalty mentioned above.  It does look, on replay, that Skuta’s was closer to legal than the referees thought, an opinion backed by former NFL ref Mike Pereira on Fox’s broadcast.

Every team, however, can point to a penalty or three and say that this should have been called another way, or that it wasn’t really a foul when looked at with the benefit of super slow-motion, high-def replays.  It is part of the game, unfortunately, and while these sorts of things should be reviewable, the fact is that it more or less evens out over the course of the season.

How big of a problem are the 49ers' penalties?  In a vacuum, huge, but there could be mitigating factors.  Perhaps the 49ers have had a set of penalty-happy referees, which will even itself out over the course of the season.  Perhaps the 49ers have had a higher-than-normal share of borderline calls, which should even itself out over the season.  Perhaps most of the 49ers penalties have been the results of good play rather than stupid mistakes.  Let’s look at each of those three cases to see if the 49ers' gross penalty count is at all misleading.

Are the 49ers getting flag-happy referees?

Pro Football Reference keeps a record of all NFL referee crews and how many flags they’ve thrown.  Because three games is a relatively small sample size, I’m going to use flags per game over each referee’s career to see if there’s a trend for a greater or fewer number of flags.  Pro Football Focus (subscription required) also evaluates if each ref throws more or less flags per game than average, based on each year’s average, so I’m including that as well.  The 49ers’ three referees have been Carl Cheffers, Terry McAulay and Gene Steratore:

Referee	2013	2014	Career Avg	Pen/G Delta
Jerome Boger	210	37	13.47	+1.06
Carl Cheffers	204	56	13.17	+0.72
Ed Hochuli	187	33	13.2	+0.71
Jeff Triplette	211	32	13.09	+0.60
Brad Allen	-	43	14.33	+0.56
Terry McAulay	195	45	12.94	+0.45
Tony Corrente	173	57	12.83	+0.34
Walt Anderson	211	32	12.81	+0.32
John Parry	206	45	12.75	+0.30
Craig Wrolstad	188	40	12.57	+0.10
Ronald Torbert	180	50	12.06	-0.33
Bill Leavy	182	30	11.89	-0.60
Gene Steratore	197	41	11.87	-0.60
Walt Coleman	211	19	11.88	-0.61
Clete Blakeman	189	32	11.47	-0.66
Pete Morelli	153	35	11.76	-0.73
Bill Vinovich	179	36	12.05	-0.74

Well, two of the 49ers refs—Cheffers and McAulay—have been historically rather flag-happy, but Steratore has been often satisfied to keep his flag in his pocket.  Streratore was the one working the Arizona game, and the number of flags did in fact go down.  The 49ers were flagged nine times against Arizona compared with 16 times against Chicago (Cheffers) and 11 against Dallas (McAulay).  The most penalties came with the referee who throws the most flags.

This is somewhat verified by the fact that 49ers opponents have committed 25 fouls, with five more declined or offsetting.  That’s tied for fourth most in the league; the officials in 49ers games are flagging both teams more than the league average at the moment.

It’s worth noting that the 49ers still committed more penalties than you would expect each referee to throw in a vacuum, but there might be something to the fact that the 49ers have had a particularly stringent set of referees.  Give them Vinovich, Morelli or Blakeman, and you might see those numbers drop.  That will work itself out as the year goes by.

Do the 49ers get an unfair share of bad calls?

There’s no statistical way to prove or disprove this one without seeing the NFL’s individual grades for each of the referee crews.  Even if you went back and charted every single play a penalty flag was thrown on, you would still miss no-calls.

USA TODAY Sports

My gut reaction, however, is no.  For every call I disagree with against San Francisco, I can find others affecting other teams—note Percy Harvin stepping out of bounds on a touchdown, for example, or DeSean Jackson not getting flagged for slamming Malcom Jenkins in the face.  The 49ers also have benefited from officiating errors—they scored a touchdown against Chicago despite the play clock hitting zero.

It’s human nature to focus on bad calls against your team when they’re losing, but I don’t think there’s any real evidence to support an argument that the 49ers are getting more than their fair share of poor calls.

Are the penalties harming the team to begin with?

Any penalty can hurt a team, of course—you’re giving your opponent free first downs and yardage to march up the field.  Sometimes, a very minor, borderline call allows an opponent to score a crucial touchdown, and other times, a blatant foul ends up resulting in nothing more than a punt a few plays later.  Looking at individual penalties is not a good way to determine if they are good or bad in a vacuum.

I believe there is such a thing as good penalties and bad penalties in general, however.  Football Outsiders research has shown that while there is a correlation between offensive penalties and losses, there is not a correlation between defensive penalties and losses.  Defensive penalties are often indicative of good play, not bad—I’ll let them explain further:

"

Cornerbacks who play tight coverage may be just on the edge of a penalty on most plays, only occasionally earning a flag. Defensive ends who get a good jump on rushing the passer will gladly trade an encroachment penalty or two for ten snaps where they get off the blocks a split-second before the linemen trying to block them

"

San Francisco has 15 offensive penalties and 21 defensive penalties this season.   Most notable on defense are five instances each of illegal contact, unnecessary roughness and illegal use of hands—only two flags have gone their way all season long.

While I agree with Football Outsiders that occasionally defensive penalties come from playing hard, there is a limit here, and the 49ers are definitely pushing it.  Are they getting more flags than their opponents because of bad luck, or are they actually pushing the new rules boundaries more than other teams?

I imagine it’s a little of column A and column B.   Remember, the 49ers have one of the least experienced secondaries in the NFL this season, so it’s understandable if their lack of experience means that they are overzealous at times.  I think the fact that the calls have come in such crucial situations is also a factor of random chance as opposed to an intentional attempt to commit more fouls in crucial situations.

Rick Scuteri/Associated Press

That’s not to say that it’s not a problem at all.   On defense, Ahmad Brooks has been caught with illegal use of hands twice, and a veteran of his caliber should know better.  Similarly, Patrick Willis has been flagged three times—unnecessary roughness, roughing the passer and illegal contact.  While you can argue whether or not some of those fouls should have been called, you also have to remember that Willis was never flagged at all in 2013, so this is somewhat out of character and needs to be fixed.

I’m more concerned about the two tackles on offense than I am anyone on defense.  Jonathan Martin is a backup, so his clipping and false start can be fixed by getting Anthony Davis back in the lineup.  Joe Staley, however, has been caught holding twice and for a false start one more time.  That’s more penalties than he got all of last season, and he’s got to get that under control, too.

Don’t Panic Just Yet

To sum up, the amount of penalties the 49ers have committed is definitely troublesome, but the raw numbers make it look worse than it actually is.  The 49ers have had a series of some of the harsher referees in the league, and their penalties dropped when going up against one of the more lenient.  Most of the penalties on defense are a result of hard play as opposed to boneheaded decisions, and the repeated offenders are players who have historically known better and will probably return to their historical averages soon.

It’s a problem that needs to be solved, and soon—but it’s a problem that’s less of a mountain than it appears just by looking at the flags.

Bryan Knowles is a featured columnist for Bleacher Report, covering the San Francisco 49ers.  Follow him @BryKno on twitter.