If your Clan Castle is empty when it should be full of troops, check your battle log to make sure they haven’t been used either for attacking or in defense. Also, make sure you have not accidentally deleted them.

If you’re missing only a few troops, or your castle no longer accepts donations even though it still has space, it’s because you have received bigger donations than your Clan Castle can hold. The troops that did not fit into your castle will be queued, moving in after you've deployed the others.