One of the big plays of the game saw 49ers QB Colin Kaepernick scramble back and into the end zone, throw away the ball and get called for intentional grounding because the ball reportedly did not reach the line of scrimmage. It turns out the ball actually did get to the line of scrimmage (17 yard line) but out of bounds. The grounding rule allows for the line of scrimmage to extend out of bounds, so a pass that gets past the line out of bounds should not be grounding. The refs called it and that was a mistake on their part.
The problem was that they told Jim Harbaugh he could not review the play. Although the Rams scored on the play, the head referee told the media after the game that "The result of the play is not a scoring play, it's a penalty enforcement that results in a score." Scoring plays are required to be reviewed, while penalties are not allowed to be reviewed. Jim Harbaugh appeared to want to challenge the play, holding the red flag in his hands, but the refs apparently told him otherwise. Had he thrown the flag, I'm pretty sure the 49ers actually would have been penalized 15 yards on the ensuing kickoff for challenging a play that cannot be challenged.
This does not make us feel any better about the ref's poor call to start this, but this is for clarification purposes. I put together a recap video and at the 1:24 mark you can see the play in question and where the ball lands. Of course, I think the first line of the video sums this up fairly well.