Timeouts

I don't think I'm alone in feeling that HCCM still has a learning curve on managing his timeouts. That being said, I have a couple of questions?
1. On the fateful last drive, JMU had a pass for about 8 yards over the middle and the clock should have kept running, but the JMU player stayed down with an injury. JMU did not call timeout, but the clock was stopped. Shouldn't they have been charged a time out in order for the clock to stop?
2. Just after that play, WHY did we call timout when JMU was running around confused on offense and about to take a delay of game, or at worst need to use one of their timeouts?
3. With around a minute and change, we did call timeout after an out of bounds play. We can argue all day about the merits of calling a timeout to let your defense rest/regroup in that situation.
All that being said, we should have had at minimum TWO timeouts and arguably THREE. Having at least one of those additional time outs drastically changes how we could approach that final desperation drive, opening up the middle of the field when all we needed was a field goal.
1. On the fateful last drive, JMU had a pass for about 8 yards over the middle and the clock should have kept running, but the JMU player stayed down with an injury. JMU did not call timeout, but the clock was stopped. Shouldn't they have been charged a time out in order for the clock to stop?
2. Just after that play, WHY did we call timout when JMU was running around confused on offense and about to take a delay of game, or at worst need to use one of their timeouts?
3. With around a minute and change, we did call timeout after an out of bounds play. We can argue all day about the merits of calling a timeout to let your defense rest/regroup in that situation.
All that being said, we should have had at minimum TWO timeouts and arguably THREE. Having at least one of those additional time outs drastically changes how we could approach that final desperation drive, opening up the middle of the field when all we needed was a field goal.