The defense in particular gave up touchdowns instead of field goals, including the first drive of the game. The 49ers had been used to playing with a lead in 2012 prior to the Vikings game and they didn't seem to respond well to being down early.
Against a Jets run game that hasn't scared anyone, I look for the defense to recover this week. Shonn Greene has struggled and may lose touches as early as this week. Mark Sanchez has returned to Earth after a big opening week and the 49ers should look to fluster him early and often.
One thing I hope to see soon is the return of the pass rush. Either teams have gotten keen to the 49ers tricks or the front seven simply lacks the same tenacity as last season...but the results haven't been near as good in 2012.
Lastly, the pass coverage by second-year outside linebacker Aldon Smith will need to improve...otherwise Vic Fangio will have to use other coverages and try to keep Smith near the line of scrimmage where his skills better translate. Sometimes I wonder if the defense isn't better off in their Nickel package where the OLBs can simply worry about the run or rushing the passer.
All of these things will play-out for the defense Sunday in New Jersey. Until then I know we'll all be eagerly awaiting this next chapter of the season.