For admins new to configuring Intune updates in the publisher it may be confusing to see different assignments when looking at the assignments window based on how the user accessed the window. For example, right clicking an app/update shows you the assignments PMPC will touch during a sync. Opening the assignments window from the product list accessed via the cloud icon shows you a live view of assignments. In this view there is no indication which assignments PMPC is managing and which are not.
Adding a banner, modified title to the window or some other indicator to indicate the difference could help avoid having unnecessary support cases open. (As I did misunderstanding what I was looking at because there was 1 assignment being managed but 2 assignments on the product when viewing the live data).