Twice today I have been in a rally for level 5 giant. Both times the giant disappears and it cost..

Giants can disappear if their spawn timer runs out. You can see the timer by tapping on them. The person who set up the rally will see a warning if their rally time will exceed the spawn timer though.

They can also disappear if another rally kills them first. Its possible for any other player in the province to also set a rally on the same giant, and if it is a shorter rally time then they may march and kill it first. If you are in an area with lots of other players then this may be more likely to happen but twice in 1 day would be very unlucky.