Have you tried "shift + left clicking" the unit/vehilce under the waypoint to select it, change its properties?

upvoted, eventhough it isn't a major issue, it is annoying.

The biggest annoyance is you cannot move/delete either the unit or waypoint, you must delete both and start over.

Holding left shift give you access to units beneath waypoints.

For example to edit a vehicle with a waypoint ontop of it, just hold left shift and then double-klick it.

Holding shift lets you edit units under waypoints.