Near the end of the first half in Super Bowl LIV, coach Kyle Shanahan and the 49ers faced a choice.

Just under a minute -- 59 seconds to be exact -- remained and the ball was at the San Francisco 20-yard line. Shanahan elected to run the ball twice for just five yards, burning 39 seconds off the clock before the Kansas City Chiefs elected to call their first timeout.

All of a sudden, Shanahan switched up the strategy and went to tailback Jeff Wilson Jr. for 20 yards, followed by a 42-yard completion to tight end George Kittle that was waived off after a controversial pass interference penalty on Kittle.

Nonetheless, San Francisco missed a crucial opportunity to score some points before the half, points that might have turned the tide in an eventual 31-20 win for coach Andy Reid and the Chiefs.

As ESPN’s Mina Kimes pointed out on the “ESPN Daily” podcast, this isn’t the first time some questionable clock management has cost the 49ers in a big game.

“He’s undeniably one of the most forward-thinking coaches in the NFL,” Kimes said. “But he does sometimes have a tendency to manage the game a little conservatively.

“I was reminded of the 49ers game against the Ravens this year. At the end of the first half, he mismanaged the clock a bit, and they ended up having to try for a long field goal, and lost 20-17.”

This was the sequence I brought up on this morning’s podcast—went back to see how Shanahan defended it, and he said they wanted to bleed more clock, then wait for for the one minute mark to push it. 🤔 https://t.co/y7P8WGQLzp — Mina Kimes (@minakimes) February 3, 2020

Once again in that Week 13 loss in Baltimore, the Niners had just under two minutes and three timeouts, and elected to burn the clock all the way down to 15 seconds before using the team’s first timeout.

But Shanahan’s propensity to play conservatively doesn’t just extend to the clock.

San Francisco attempted the second-fewest fourth-down conversions in the NFL this season, ahead of only Kansas City ironically.

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While he has shown signs of being a transcendent play-caller in the NFL, Shanahan's misuse of the final two minutes in part cost his team two crucial games this season, including the Super Bowl.

We’ll have to wait for the 2020 NFL season to see whether Shanahan has adjusted his mindset in any way.