For the first time under Jim Harbuagh, the 49ers have lost back to back games as they were beaten badly by the Colts 27-7 in Week 3. Also for the first time under Harbaugh, the team looks like a disaster as the offense was barely competitive for the second week in a row. There are real question marks in San Francisco right now and the team looks nothing like the playoff contenter most thought it would be coming into the season.

Vernon Davis was missed

Anyone who has ever doubted what Vernon Davis means to the 49er offense only has to turn on the game film of this loss to realize how important he is. Even when Davis isn't filling up the stat sheet, just his presense in the lineup commands the attention of the defense. Because the opposing defenders have to account for Davis at all times, it allows other players to get open and make plays. Without him against the Colts, the other 49er receiving options could not get any separation from an Indy secondary that was torched at home by Ryan Tannehill in Week 2 for 319 yards.

Lack of options at receiver

The 49ers simply do not have an effective wide receiver opposite Anquan Boldin. While Kyle Williams is a nice role player, he has not proven to be starting material. In the first three games of the year, Williams only has nine receptions for 87 yards. Beyond Williams, Marlon Moore and Quinton Patton have one catch combined (Moore) for six yards. In the past two weeks, all 49er wide receivers have 13 catches for 131 yards and no touchdowns.

This probably shouldn't come as a surprise given the track records of Williams and Moore. The two only have 47 career catches combined and have at no point in their careers distinguished themselves as legitimate NFL first teamers. While Patton has underwhelmed so far, it's not realistic to think a rookie who was taken in the fourth round would make an immediate impact. The 49ers have to figure something out though, and soon, or the woes in the passing game will continue.

Gore needs to be focal point

It's inexcusable that in a game that was 13-7 going into the fourth quarter that Frank Gore only had 11 carries. The Colts came into the game with the sixth worse rushing defense in the league having given up 272 yards over the first two weeks. The 49ers gained 115 yards as a team on 23 attempts but 7 of those were Kaepernick scrambles or runs. That means they only handed the ball to their backs 16 times.

With the passing game struggling, the offense should have been centered around Gore and Hunter. Instead, Greg Roman continues to appear like he wants the 49ers to be something their not which is confusing considering their approach and commitment to the run the past two seasons.

Kaepernick's play is concerning

It's entirely possible that there really is no one open and 49er receivers can't gain separation. It could be that even Peyton Manning would have trouble moving the ball with only Anquan Boldin as a real option. All of that could be true, but it does not change the fact that Colin Kaepernick has been terrible over his last two starts.

Kaepernick continues to look indecisive and does not appear to be seeing the whole field. When plays break down, he's at times trying to force throws instead of using his legs and has left first downs on the field because of it. Against the Colts, Kaepernick only threw for 150 yards and that stat line is generous considering how much of it was in garbage time. He is 26 of 55 (47 percent) with 277 yards and no touchdowns the last two weeks. He has been intercepted four times over that span as well. We all knew (or should have) that there were going to be some bumps in the road this season as Kaepernick matured but I'm not sure anyone could have seen this coming.

Luck a cut above the rest

For all of the talk about Kaepernick, Russell Wilson, and Robert Griffin in the media, it's sometimes easy to forget that Luck is better than all of them. He took an inferior Colts team on the road in week 3 and executed his game plan perfectly. Luck's stats were not eye popping (164 yards passing and one rushing touchdown) but he kept the chains moving and kept the 49er defense on the field. The Colts dominated the time of possession and held the ball for over 36 minutes.

Defense needs a game changer

For most of the game, the 49er defense did enough to win. They kept the score close but got no help from the offense who could not sustain any kind of drive. While the defense is still one of the better units in the NFL, they lack two main components that had made them elite in the past. The first is a consistent pass rush from anyone not named Aldon Smith. The 49ers have seven sacks through three games and Aldon has 3.5 of them. No other player has more than one. Because of that, there seem to be long stretches when oppossing quarterbacks have clean pockets and more than enough time to make their reads.

The second component they lack is forcing turnovers. Eric Reid is the only 49er with an interception (he has two) and the defense is not making game changing plays that swing momentum. That could be directly related to the lack of consistent pressure but a short field or two would do a lot in helping the offense get some easy points.

What's next?

The 49ers have to try and get things figured out on a short week as they play the St. Louis Rams on Thursday night. If Davis is not able to suit up expect some of the same problems to show up on offense. The Rams gave the 49ers fits last season and the game has, unexpectedly, become a must win for a reeling Niner's squad.