So I have this game on Steam

When I play a game, I play it manually and then play it down to 0.00 on the clock

then when I exit the playcalling screen the game never shows up on the boxscore schedule page. I have to then sim the game for a different result than I had when I played it manually. What gives?

I haven't been able to reproduce this. As soon as you click the X in the top right corner it closes the game and sims whatever you hadn't played out. I guess I'd need more information on what you were doing at the end... maybe there is a case I'm missing. I'd need to know whether you were on offense or defense, what play you were running, or whether you were doing some sort of spike, FG, etc.