See FMovieSceneSpawnRegister and FLevelSequenceSpawnRegister which are capabilities.
Once a sequence is finished FSequenceInstance::Finish is called.
if the sequence is a root sequence FMovieSceneSpawnRegister capability will be queried.
If it exist FMovieSceneSpawnRegister::ForgetExternallyOwnedSpawnedObjects and FMovieSceneSpawnRegister::CleanUp are called.
This will process to destroy the object that were spawned and that should be destroyed (usually the objects that are marked as owned by the sequence that spawned them). See FMovieSceneSpawnRegister::DestroySpawnedObject.
The real destruction code should be in UMovieSceneSpawnableBindingBase derived classes using the DestroySpawnedObjectInternal pure virtual.