2. Kyle Shanahan's coin toss decision never made sense
The decision to receive on the first possession of overtime made absolutely no sense at the time and looks even worse now. The 49ers won the coin toss, giving them the prime advantage to defer and see what the Chiefs managed to do offensively. Shanahan inexplicably chose to instead give Andy Reid that edge, and the Chiefs wound up taking advantage of it.
The new overtime rules guaranteed possession for both teams. In previous years a team would win the game after scoring a touchdown in overtime regardless of whether the other team touched the ball or not, like the Patriots against Shanahan's Falcons. This year, however, even if the team that received scored a touchdown, the opponent would be able to match it and keep the game going.
The Niners opted to take the ball first, going in completely unprepared and giving the Chiefs all the information they'd need. Sure, Shanahan would've gotten the ball first if both teams scored touchdowns with a chance to win the game, but the Chiefs said after the game that they would've gone for two -- most other teams likely would too -- instead of putting the game in Patrick Mahomes' hands.
By electing to receive, Shanahan put his defense in a horrific spot, needing to hold Patrick Mahomes to a field goal just to keep the game going with unlimited time and the Chiefs in four-down territory throughout the entire drive. Playing for a third drive which they weren't guaranteed to get is just not smart. It made no sense at the time and looks even worse after watching the ending of the game unfold.