http://iscoresports.com/

When I have a play where there is essentially a dead ball foul (defensive offsides or encroachment), I have been noticing that the individual play entry says something along these lines "#10 Bob Jones takes a knee. Penalty on the defense #52 Jim Smith, offsides, repeat down." The problem I see is that this appears to be a carry and could count against the QB's rushing stats. Is this so, and is this fixable?

If you are entering the play as a player taking a knee, then yes, it is a carry.

If you select the Penalty button from the main scoring screen (instead of Run or Pass), it will then let you enter the penalty, and you will wind up with just the penalty and no player taking a knee.