That is really odd, I need to dig and see if I can figure out why that happened.

Solved it -

He didn't score the touchdown, he was inches short. Also, the clock was at 0, so the half was over. They accepted the penalty to have one more play before the half.

Nah, the play I am referring to there is time on the clock when the play (with the offsides pen) finsihes, we then run another play.
Yes the play with the pen runs all the way , to what I'm guessing would have been 1st and goal (inches). We should have declined that penalty and gone from the 0-goal-line with the remaining seconds. For me this play is not right.

edit: Ok just wtched it again and the play clock does run down to 0 on the penalty play, but then we run a play again and 1 second is back on the clock, somehow. Ha ha I'm getting confused as to whats happened now

The half can't end on a defensive penalty, so there is one untimed play (I'm putting one second on the clock for the untimed play so the game engine doesn't end the half)

OK thanks for clarifying that