This came up in a game last night and unsure how to resolve for future games! The Rebel player wanted to "Incite Rebellion" and Start an Uprising. However there were no Troopers or Airspeeders left in his pool of troops! We couldn't seem to find an answer in the rules so just allowed him to move some units around to action the mission (Probably wrongly!!). How should we rectify this situation in the future?

The rules state that units are limited to those supplied. So he would not gain any units in the system.

I believe a player can elect to destroy their own units so I think he could destroy units, returning them to the supply and then perform the mission.

I would say that the Rebel can only destroy units in the Refresh phase. At that point you already have the mission card and should plan accordingly.

Of course, if the Rebels are hitting their component limitation, they are probably going to win anyway.

Yes, you have to destroy them in the refresh phase

I ran out of Mon Cal Cruisers (built two and used the Mon Cal Mission for number three), and couldn't build a fourth when allowed during the final turn, and I ran out of Speeders many times. But, those were the only two units I maxed out on. I really pushed hard to gain Mon Cal early, because I like big boats and I cannot lie.