If world composition is in enabled and an instance static mesh actor has been added to the scene the level will remain dirty after compiling.
Result: The pop up to ensure that you would like to save changes for the level will pop up everytime the save all button is used
Expected: The level would no longer be dirty after saving (if no changes have been made)
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-52753 in the post.