OK, so I found out what the "problem" was, but it's not a problem, it's a design intention. Maybe this will help someone else...
When you create a mission in the Mission Hub, all waypoints automatically are pointing North (0 degrees).
Any waypoints that are set to 0 degrees will automatically point to a new POI that you drop on the map.
Litchi implied this was a design intention (although I told them I felt it was more of a bug/hinderence), but oh well.
To work around this, all you have to do is to change any waypoints you don't want to follow/point to a new POI by at least 1 degree (ie: 359 or 1 for "almost North").
That way, anytime you drop a POI on your mission map, as long as none of your WP's are set to 0 heading, they will stay fixed (unless you change a WP to point to a POI purposefully).
Oh, while I had their attention I asked if they'd consider adding colors to POI's and associating any WP's with the same color if they are pointing to that particular POI.