I'm just going through the Game Log here and I'm noting down what appeared to be the mistakes here.
4-3-SD 39 (10:31) 5-M.Scifres punts 58 yards to DEN 3, Center-47-M.Windt. 19-E.Royal to DEN 17 for 14 yards (98-A.Barnes).
This one is not a big deal, but Royal should have let the ball bounce into the end zone. It's only three yards, but there's a psychological disadvantage to being caught inside the 20. I suppose it's possible that Royal could have seen that the ball was pointed in such a way that it might have been downed inside the five, but still - at this point I would list it as a special teams mistake on an offensive player.
2-12-SD 28 (7:39) 35-M.Tolbert up the middle to SD 45 for 17 yards (23-R.Hill).
Ugh - giving up a long run when they've got a long down is tough to swallow. I don't have the footage in front of me, but I remember we had a fair amount on the line, San Diego stunted with some pulling, and they opened up a huge hole in the middle. Hill made the tackle, but that means that the failure was on someone else, probably on a middle linebacker?
4-14-SD 41 (6:04) (Punt formation) 5-M.Scifres pass deep middle to 35-M.Tolbert to DEN 31 for 28 yards (19-E.Royal).
It's hard to blame Decker for not having man-to-man coverage skills, but the team definitely should have been more prepared for this. No one was rushing the punter and he had loads of time. Still, if a team is going to pull a stunt like that, it's going to work sometimes.
3-1-DEN 22 (3:55) 35-M.Tolbert up the middle to DEN 9 for 13 yards (55-D.Williams, 33-N.Jones).
Converting a 3rd-and-1 is more likely than not, but... 13 yards? I don't know whose failure this one was, but it's again bad, undisciplined football, more reminiscent of late 2009 than most of our defensive play this season. On to the 2nd quarter...
3-3-SD 39 (14:18) 8-K.Orton pass short left intended for 10-J.Gaffney INTERCEPTED by 20-A.Cason at SD 32. 20-A.Cason to DEN 40 for 28 yards (84-B.Lloyd).
Orton was caught with his pants down on this play. He telegraphed his intentions and rushed his throw due to oncoming pressure, you could tell by his delivery. It looked like childs play for the DB to jump the route. I'd have to know the play design to know if Clady screwed up or if Orton was supposed to do something different. Luckily, a missed San Diego field goal meant a first down only 19 yards further back down the field.
1-10 SD 38 (12:00) 35-L.Ball right end to SD 37 for 1 yard (74-J.Cesaire).
I remember this run - Ball looked slow to the line of scrimmage and it didn't look like he made the right cut. All of a sudden you're in 2nd-and-9, and on the next play, Orton was sacked on a good play by Phillips, effectively killing the drive.
2-9-SD 14 (9:54) 17-P.Rivers pass short left to 12-P.Crayton to SD 30 for 16 yards (32-P.Cox). PENALTY on DEN-98-R.McBean, Face Mask (15 Yards), 15 yards, enforced at SD 30.
1-10-SD 45 (9:27) 17-P.Rivers pass deep left to 12-P.Crayton pushed ob at DEN 6 for 49 yards (23-R.Hill).
1-6-DEN 6 (8:54) 22-J.Hester left end to DEN 2 for 4 yards (55-D.Williams, 51-J.Mays). PENALTY on DEN-99-K.Vickerson, Unnecessary Roughness, 1 yard, enforced at DEN 2.
This three-play sequence told the story of this drive. At the time, the game was tied, but this led to San Diego taking the lead. It looked like a linebacker or nickel back was in the wrong zone, Cox got beat on a good play by the receiver, and then Hill did a really poor tackling job. They just didn't look ready on this drive.
3-3-DEN 34 (6:33) 8-K.Orton sacked at DEN 23 for -11 yards (95-S.Phillips).
This was the ensuing drive, and it meant a 3-and-out immediately after going down 14-7. This was a playcalling mistake - it was that silly reverse pass, and it was a horrible time for that playcall, at a time when you just need to be methodical. This was a key point of the game, momentum-wise. You don't double down when the other team has the advantage, you play methodically to get back into the game.
We followed this up with a bad punt, but then one of the really good defensive series of the game - a sack by Bannan, and an interception by Bailey, presumably to make up for the previous poor defensive series.
Unfortunately, we had a three-and-out right afterward, that didn't seem to have any real mistakes, just good execution by the San Diego defense.
1-10-DEN 40 (2:15) (Shotgun) 17-P.Rivers pass short left to 12-P.Crayton for 40 yards, TOUCHDOWN.
This was a plain old missed screen tackle by Dawkins. He just missed it. This is unfortunate, Dawkins was playing at a high level last season, and maybe for the first couple of games this season. Unless he's secretly injured, it looks like he's really lost something.
2-10-SD 38 (:46) (Shotgun) 8-K.Orton pass short right to 28-C.Buckhalter to SD 40 for -2 yards (93-L.Castillo, 90-A.Applewhite). PENALTY on DEN-88-D.Thomas, Offensive Pass Interference, 10 yards, enforced at SD 38 - No Play.
It's 2nd and 10 and we have a chance to cut the score to seven. Instead, we throw a short pass (why?) to Buckhalter (why?). In addition, there's an OPI penalty - I'm not sure if the penalty was a good call, but any way around it, this was not a good moment in the game. This was followed on 2nd and 20 by yet another short pass attempt to Buckhalter. It's no wonder Orton was sacked on 3rd down. Why throw to Buckhalter two plays in a row while ignoring the first down marker? This is where discouragement is clearly having an impact.
On to the 3rd quarter...
3-9-SD 43 (12:47) (Shotgun) 17-P.Rivers pass short middle to 43-D.Sproles for 57 yards, TOUCHDOWN.
This is again Dawkins, he was just burned on the play. It actually looked like he gave up on the play before he realized that Sproles beat him. We also blitzed way too many people here - there should have been more nickel or dime help in the secondary.
At this point, the game is basically over. There are some ticky-tack things - a false start on Harris, a 6-yard pass to Graham on 3rd and 13, and an encroachment on Vickerson, but things are basically settled at this point.
My summary? We had a little bit of special teams difficulty at the beginning, like the fake punt, but that's the sort of thing a team should be able to absorb. Maybe you give Orton an interception once in a while, maybe you give a defense a couple of long pass plays when you're playing Rivers. But, beyond that, the real problems were our poor defensive discipline, a seriously slowing-down Dawkins (he gave up two touchdowns for 97 yards on two plays), and some weird offensive playcalling that looked stubborn, like doubling down on a bad hand. Also, I missed it in the game log, but it didn't seem a good idea to put Tebow in when he came into the game - it slowed down a drive. And, I can't help but think we have a serious talent problem somewhere in the shallow-secondary deep-linebacker section of the field, or maybe that is a scheme problem. When you run a 5-2, you're putting a lot of pressure on your secondary, and I don't think we can say the secondary is the strength of our defense anymore.
What would have helped in this game? Less blitzing in favor of stunts - remember when we beat them up last year with delayed A-gap blitzes? - more (or better) nickel/dime help, and scaled down responsibilities for Dawkins. I think that would have meant a closer game. I'm not sure what to do about the run defense and Tolbert, though. It may be that the health of our linebackers is hurting us there.