A flagship's special ability to ignore one red alert does not work when the flagship is on an asteroid, planet and other space features. The same rule is effect for other units that have the special ability to ignore one red alert.
Stars can be used to buy off (ignore) one red alert and combat cards can be used for these units that lost there special ability to ignore one red alert when on a space feature.
https://boardgamegeek.com/thread/2196239/article/31892040#31892040