With 1:53 left in the first half of Super Bowl LIV, and the score tied 10-10, the 49ers stopped quarterback Patrick Mahomes and the Kansas City Chiefs' offense on third-and-14. And then, coach Kyle Shanahan made a controversial decision.

The 49ers still had all three of their timeouts left, but Shanahan opted not to use one. The clock went from 1:47 to 59 seconds left as the Chiefs drained 48 seconds and punted the ball into the end zone.

Shanahan could have called the timeout at 1:47. Now, the 49ers are going to get the ball at the 25 with 59 seconds left — Jonathan Jones (@jjones9) February 3, 2020

It's safe to say 49ers general manager John Lynch didn't agree with Shanahan's decision. Lynch was calling for a timeout from his luxury box, but Shanahan clearly wasn't in sync with the GM.

Shanahan stayed conservative and ran the ball for only five yards on the 49ers' first two plays after the punt. Quarterback Jimmy Garoppolo did later connect with tight end George Kittle on a perfect 42-yard pass, but the referees called a controversial offensive pass interference on Kittle.

[RELATED: Report: 49ers could extend Shanahan, Lynch by September]

Jimmy G took a knee on the next play after the penalty, and the 49ers and Chiefs went to halftime with the score tied at 10 points apiece.

Lynch and Shanahan have been on the same page since taking over the 49ers before the 2017 season. They slowly built a star-studded roster to reach the Super Bowl, however, they were far from on the same page in a critical moment Sunday against the Chiefs.