Maybe a network connection issue?
You can contact the disney support though. Perhaps they can do something about it.
Does this happen every time?
I am using the Android version and missing troops in transports occur only very rarely. Usually when the game lost connection to the server somehow.
(Rebels/Android/iOS). Just PM me here/LINE:lleyleber or request in game with a meaningful text. If you want to take part in wars, lv7+ is useful.