Combat super crisis cards during final jump in the Pegasus expansion
No. From the rulebook (pg. 15):


  During the Prepare for Jump step of every subsequent New Caprica Crisis Card, when an evacuation icon appears, the current player takes one civilian ship from the top of the Prepared Civilian Ships stack and moves it to any space area with a viper launch icon.


There's no mention that it can happen any other way.

To be honest, I'm surprised that there is even a combat set-up card in the New Caprica Crisis deck that would have a civilian ship on it, although I don't have it in front of me to check. Can you show an example of the card you mean?

I wonder if you've switched back to the regular Crisis deck after Galactica returns? You should be continuing to use the New Caprica Crisis deck. Additionally, just some extra info from pg. 16:


  During the New Caprica phase, ignore any effect that would place, destroy, or move ships in any space area around Galactica or centurions on the Boarding Party track, until the Galactica returns to orbit (see page 17).