I use a lot of waypoints, whether for building fleets, staging areas, or upgrading starbases with multiple constructors automatically. I noticed that if I create enough waypoints to cause the waypoint list to spawn a scroll bar, the bar won't move and I can't access the waypoints scrolled off the page.
A feature request I'd like to add is that you can manage waypoints (delete them) from a list, rather than have to select them individually on the main screen and deleting them.