is that one of the missions within advent city centers where Central command tells you during the mission that interceptors are inbound fast and you need to extract within the time window or the mission is a bust because your small bird will be blown out?
Ok so the skyranger is shot down and you are caugth in the city trying to escape, that sounds like the best part of mission. When you end a mission prematurely because of a gameplay feature, in this case the timer, that's just bad design. Specifically when there is a disconnect and it doesn't feel like it should end.
It's like when you have to reload a babysitting mission because the target died, or the stealth missions in Ascreed where you 'die' when you are discovered. No, no no. Those things are results that you (game designers) were to lazy to show me.