What happens if a game ends on extra innings and a player coming home to end the game, doesn’t step on home plate?
Extra innings aside, Rule 5.09(b)(12) states:
[Any runner is out when:] In running or sliding for home base, he fails to touch home base and makes no attempt to return to the base, when a fielder holds the ball in his hand, while touching home base, and appeals to the umpire for the decision;
This happened in the Minor Leagues in the 2019 season when Miguelangel Sierra hit a home-run, but failed to touch home plate. The opposing team (Down East Wood Ducks) called for an appeal, and Sierra was out, no points were granted.
If a player misses any base, it is up to the fielding team to appeal the call to the umpires. If an umpire sees a player miss a base, they do not call them out, it is up to the opposing team to appeal, by stepping on the base while holding the ball, or tagging the player. If the appeal is successful, the runner will be called out and the run will be disallowed.
This is why umpires only call players safe if there is an attempt to get them out. If a throw comes in very late, or does not come in at all, the umpire will not call a runner safe at a base.