This is working the way ACF has always worked. The values from the fields that are removed are not deleted from the database.
You can probably see this on a repeater field as well, if you add 3 rows and save and then remove one of them the 3rd will probably linger. ACF currently does not have the ability to remove data from fields that don’t exist when saving the form. It only inserts and updates fields that are submitted.
If you want data that is no longer needed to be deleted you would need to create an acf/save_post action http://www.advancedcustomfields.com/resources/acfsave_post/ and delete the data yourself.
