I have made a slight change to the site to attempt to fix this issue. Going forward, if a player in your lineup is in an in-progress game, that will count towards the game cap. If that player never enters the game and has an official stat of 0 minutes for that game once it is final, you will be refunded that game for your weekly game caps.
This should close a loophole / race condition where a player coming off the bench has not entered the game yet and another game starts and when the player coming off the bench enters their game a team is now able to go over their game limits for the week.
The clue for this solution came from this post from last year:
Now you should lose that game remaining on that lineup slot immediately upon the game starting and will be refunded it if the player never enters the game.
I’m not marking this as ‘resolved’ quite yet and continue to investigate / keep an eye on things.