After the San Francisco 49ers got manhandled at home Sunday afternoon by the Indianapolis Colts, many fans and experts are asking themselves: what’s wrong with the 49ers?

Although the season is only three games in, the Niners have a few major red flags.

First off, they are not playing with their full team. As it does in all sports, injuries play a huge factor in every team’s success.

Before the season started, wide receiver Michael Crabtree went down during summer in Organized Team Activities with a torn Achilles tendon.

Last season, Crabtree was the Niners’ leading receiver and really seemed to click with now starting quarterback Colin Kaepernick during the team’s Super Bowl run.

Along with Crabtree, you can add cornerback Chris Culliver, nose guard Ian Williams and troubled all-pro linebacker Aldon Smith to players who will miss significant time this year.

Despite the 49ers flat out stealing Anquan Boldin from the Baltimore Ravens for a measly sixth round draft pick, the receivers are failing to get open and give Kaepernick opportunities to make plays with his arm.

The Niners lost the last two games and Kaepernick combined to throw for 277 yards, no touchdowns and four interceptions.

Not throwing a touchdown in back-to-back weeks is not going to get it done.

So you’re probably saying to yourself, if the Niners can’t throw the ball then they must be running it right?

Wrong.

In the past few years, the 49ers have been looked at as a power running team with massive offensive lineman creating huge holes and physical running backs fighting for extra yards after contact. Not to mention, the threat of Kaepernick taking off and burning teams with his legs. Just ask the Packers about that.

But so far this year, that has not been the case.

After three weeks, the 49ers are ranked 19 out of 32 teams in rushing with a four yards-per-carry average.

The Niners have only attempted 77 rushes this year, while Kaepernick has thrown 94 passes.

These stats are maybe a little biased since the Niners were down big against the Colts and in week two against Seattle, but it’s almost like they forgot what made them so successful in recent times.

On Sunday, 49ers running back Frank Gore racked up 67 yards in the first quarter and helped lead the 49ers to their only scoring drive.

After halftime, Gore only received three carries for 12 yards after having a productive first half.

According to multiple reports, Gore had some choice words for 49ers head coach Jim Harbaugh about not giving him the ball.

Between receivers failing to create plays and the running game almost being forgotten about, the 49ers have only produced 10 points in their last two weeks.

Good luck winning games averaging five points a week.

Lastly, the Niners are hurting themselves with penalties. After three weeks, San Francisco is tied for the most penalties in football at 23, good for over 200 yards.

You can’t beat yourself with dumb mistakes and expect to win football games.

Although it seems like all hope is lost for the 49ers it really isn’t. It’s only week three, there are still 13 games to be played.

Last season, the Denver Broncos started off the season at 1-2 like the Niners are and ended up winning 13 games and having the number one seed in the AFC.

Also, the 49ers schedule is favorable.

Of the 13 games left, the teams combined record is only 15-22.

The Niners are a good experienced football team with a great coaching staff lead by Harbaugh. If anyone can motivate a team and rally the troops, it’s him.

So do not panic yet Niners fans, there is still a lot of football left to be played.