Suddenly, a season that looked so promising three weeks ago now appears clouded with questions.Playing with what seemed like a Seahawk hangover, the 49ers lost to the Indianapolis Colts at Candlestick Park Sunday afternoon, 27-7, to fall to 1-2.It's the first time in the Jim Harbaugh era the Niners have lost back-to-back regular-season games and the first time his San Francisco team has been under .500.After being crushed in Seattle by the Seahawks last Sunday night on national television, the 49ers had a chance to get their confidence rolling again with a win over Indianapolis, but instead the 49ers were unable to play with any consistency.Quarterback Colin Kaepernick had his second bad game in a row, completing just 13-of-27 throws for 150 yards – more than 50 of those yards coming after the game was decided -- lost a fumble that led to a late Indianapolis touchdown, threw a late interception and couldn't get free as a runner on the read-option, which was bottled up by an active, quick-moving Colts defense. It was Kaepernick's first loss as a starter at Candlestick Park.And defensively, the 49ers couldn't stop the Colts on the ground or contain quarterback Andrew Luck, who...