tl;dr: 49ers used their first two timeouts poorly in the second half.

One of the more obvious foul-ups was San Francisco's mismanagement of its timeouts in the second half. If the 49ers had any hope of coming back from down 22, it was certainly going to be close at the end, and timeouts were going to be invaluable. Colin Kaepernick, though, burned the 49ers' first timeout just before a first-and-10 play near midfield at the halfway point of the third quarter. It seemed as if he simply didn't like the play call or the match-ups because there was time left on the play clock. The second timeout was called by Jim Harbaugh to prevent a delay-of-game penalty on the 49ers' final drive that would have set up a third-and-goal from the 10 instead of from the 5. This was a debatable call. On the one hand, San Francisco would've been pushed five yards farther from the end zone. On the other, since Baltimore was taking away the run and forcing quick passes into man-to-man coverage, the extra space might've actually made things easier for the offense. Either way, that lost timeout would come back to bite the 49ers hard.

Jim Harbaugh made another mistake risking a timeout on the challenge of a first-down ruling halfway through the fourth quarter. He won the challenge, but that only set up third-and-inches, a situation that ends up being converted more than 80 percent of the time (and which the Ravens did ultimately convert). There wasn't enough upside to justify the risk that there wouldn't be enough evidence to overturn the ruling.

Had the 49ers retained all three timeouts, they would've gotten the ball back with about 1:22 to play and great field position, assuming they would've forced a Baltimore three-and-out. With two timeouts, San Francisco could have had 43 seconds left after a stop. In fact, with at least two timeouts, San Francisco would've had enough clock to kick the field goal on fourth down of what turned out to be its final possession, force a Baltimore punt, and then kick another field goal to win.

Here's how costly those timeouts were. First, consider the field goal-stop-field goal scenario. Typically, offenses needing a field goal to survive can score a three-pointer slightly more than 30 percent of the time when starting near their own 20-yard line. With about 45 seconds left to play, they can score about 15 percent of the time when starting near their own 20. If the 49ers played for the touchdown, they would have gained possession near midfield at worst. A touchdown from there with about 1:40 to play is about a 35 percent proposition, but with about 45 seconds to play, it's about 20 percent. When the 49ers called their first timeout and when Jim Harbaugh challenged that first-down ruling, it was impossible to know just how crucial those timeouts would become. These numbers, though, show just how valuable they can be, particularly when compared to the importance of a no-account first-down play in the third quarter.

There were lots of other mistakes -- not letting Kaepernick have a run option in his final four downs, the overthrown interception, the fumble, letting up during the 108-yard run, and most of the play action in the first half.

But the poor use of timeouts in the second half -- that really made a difference.

the penalties on 3rd down while on defense...giving Flacco the second chances he needed (much like the Ravens/Refs gave Aikers his second chance)