Let's get the a few key things out of the way:
1. The Seahawks are not invincible. The most frustrating part of this game was that even late into the 3rd quarter the 49ers were in the game. They just couldn't close.
2. Fumble luck sucks. The Seahawks fumbled the ball several times, none of which were recovered by the 49ers. Sometimes the ball literally does not bounce your way.
3. Jonathan Martin is a liability at RT. The degree to which Cliff Avril abused Martin merited a call to Child Protective Services.
In this game, the game turned against the 49ers in all phases. These are the turning points that put the team's back against the proverbial playoff wall.
Turning Point 1
Game Situation: First quarter, 5:39. 3rd and 8 at the 49ers 30-yard line
Play: Dig route to Boldin
Colin Kaepernick played the kind of abysmal game we're growing to expect against Seattle. He was inaccurate, skittish, and made a few poor decisions. In this case it was the right decision, but a terrible throw.
Kap does a good job with his eyes - the stripe of his helmet is looking towards the middle of the field looking for his primary receiver, Anquan Boldin, on a dig route. After a hitch step he comes over to his secondary receiver, Brandon Lloyd, on an out route.
On any out-breaking sideline route, the quarterback has to throw the ball to the outside. If you miss, you want to miss wide because if you don't there's usually a CB waiting for the ball. Brandon Lloyd actually has space against Sherman, but Kap throws a terrible ball. This is a throw Kap completes often, and he makes it look routine. In this case, he threw Sherman a gift.
Turning Point 2
Game Situation: Second quarter, 2:36. 4th and 7 at the Seahawks 25-yard line
Result: Fumble, recovered by Seattle
This play was huge, and it could have been called back. Even 13 points down, if the 49ers can close the half out with a touchdown this is a much different game. Instead, the little things that have been plaguing the team all season came back to bite them.
Hauschka fumbles the snap and still has enough time to pick it up, channel Michael Flatley, Lord of the Dance, and get the punt off. Ricardo Lockette just makes a good play, strips the ball, and Seattle recovers.
Through week 13, the 49ers are 31st in the league on punt returns (by DVOA). Perrish Cox ranks 75th out of 75 punt returners that have played in at least 4 games (via Pro Football Focus).
Jim Harbaugh was complaining to the refs (surprise!) about an illegal man downfield, but the long snapper was only 2-3 yards from the line when the ball was kicked. The NFL isn't going to call that.
This season the offense has come under fire for underperforming. Special teams can really help an offense with field position and the 49ers kick return units have been lackluster at best.
Turning Point 3
Game Situation: Fourth quarter, 13:11. 3rd and 7 at the 49ers 40-yard line
Play: Tight end leak
Result: First down Seattle
At this point, the 49ers finally had points on the board. The team started using misdirection in the form of throwback passes and play-action passes to sustain their drive. Stopping Seattle here would put the ball back in the hands of an offense only down by 13 points - an offense seemingly starting to get their rhythm.
Then came 3rd and seven.
Seattle basically beat San Francisco with three routes all day: the RB swing pass, the WR drive, and the TE leak. On a TE leak, the tight end stays in to chip the edge rusher, then leaks out to the flat to give the QB a dump-off option.
Since we can't be sure of the call we don't know who is responsible for tight end Luke Wilson. It looks, though, like Borland is playing a Seam/Curl/Flat technique. This is a common technique linebackers often use in zone coverage. Borland follows Baldwin up the seam, then let Wilson's throw take Borland to the flat. This is an odd technique to be playing here, considering Borland is between the hashes. Usually this is a technique played outside the hashes when a linebacker is responsible for the hook zone.
The other problem is that Antoine Bethea is also in the area and carries Baldwin up the seam as well, before passing Baldwin off to another zone. This is just another coverage breakdown likely caused by miscommunication. Wilson's first touchdown pass was likely a coverage breakdown as well.
The 49ers are not out of the playoff race by any stretch - they've just made their job harder from here on out. Unless the team starts executing better, in all phases, the NFC west could see another 10-6 team miss the playoffs for the second consecutive year.