The only way this makes any sense is if the scoreboard/tv clock got slightly unsynched when the refs added a second back on the clock before the start of the play. IIRC, the ref announced a reset of the stadium clock from :08 to :09.
So, while CFB clocks don't display tenths of a second like in basketball, they obviously still exist. So, if the official clock (which apparently is hidden) was actually at 9.3 seconds (showing :09), and the stadium clock is changed from :08 to :09 (which would be 9.00 seconds left) that could explain why the Scoreboard/TV clock showed :00 at the same time the "official" replay clock still showed :01, which changed to :00 fractions of a second after they claim the WMU touched the ball.
Still, I think the officials needed to have also synched up another camera angle that showed the WMU player actually touching the ball with their "official" clock still showing :01 to overturn the call on the field. You can't tell from the angle the Big10 posted when the WMU player touches the ball.