The team can’t score in the second half. Jim Harbaugh looks like he’s about to explode. Greg Roman can’t run the offense or make adjustments. Colin Kaepernick is passing too much. Frank Gore isn’t getting enough touches. The bottom line? The San Francisco 49ers have plenty of problems after three games of the 2014 NFL season, and not a lot of time to fix things before the division starts running away on them.

The euphoria of the 28-17 win over the Dallas Cowboys in the first game has quickly changed. The 49ers are struggling with the new rules, getting called up on too many penalties. In the home loss to the Chicago Bears, they gave up 118 yards on those infractions. It was 107 yards in the loss to the Cardinals. Two games in which the 49ers held the lead going into the second half. They had a big lead against the Cowboys as well that slowly withered into something a bit more respectable.

So far this season the 49ers have been outscored 52-3 in the second half. They’ve yet to score a single point in the fourth quarter this season. They’ve faced a good defense, a deceiving, opportunistic one and a very bad one to start with. There’s a trend here, and it has nothing to do with the quality of teams the 49ers are facing – it’s about the calls being made on the sidelines, the poor execution on both sides of the scrimmage line and a team that might not be the most composed and calm with a head coach that won’t stop looking like he’s about to explode on the sidelines.

One issue has been Colin Kaepernick. No, it’s not about his interceptions. He has three this season, but all came in that weird game against the Bears. He was quite good facing the Cardinals, starting out on 9-of-9 and finishing with 245 passing yards on 29-of-37, including one throw for a touchdown. He also ran for 54 yards on 13 carries. The problem seems to be the 49ers focusing a bit too much on his abilities rather than on the entire team and offense, the real reason they’ve been so successful over the last three years.

Frank Gore got 16 carries in the first game, 13 in the loss to the Bears and just six against the Cardinals. The rushes made by Kaepernick don’t look like designed plays. Despite getting Alex Boone back, the 49ers offensive line seems to crumble under the right amount of pressure, forcing Kaepernick to scramble too many times. He has great legs and speed, but that’s not how an offense consistently succeeds. It might be that the coaching staff has fallen in love too much with what their quarterback can do under pressure.

There was some talk before this season about Gore getting fewer touches. Carlos Hyde seems like a very good draft pickup and scored a touchdown against Arizona. The running game was neglected, almost ignored in the second half. Some say it’s simply because Arizona are a very difficult team to run against (allowing just 71.7 yards per game on the ground), but it could be an offensive line that was the best in the NFL until not too long ago that simply can’t create holes and blocks for the runners.

At 1-2, the 49ers aren’t in a strange place. They’ve been here last season and bounced back remarkably. Beat the teams inferior to them, lost to the better ones. This doesn’t seem like a Super Bowl bound team at the moment. Not a special team in any aspect. In the off-season, the rumors about Harbaugh not getting along with the front office and his locker room problems seemed like rumors, nothing more. With every loss and every new weakness in this team exposed, it comes to mind that maybe there’s some truth to the crumbling aspect of coaching authority on this team.

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