I think I may have run into a bug with this mod.
I'm playing career mode with version 1.8.1.2694 and both DLCs, and just came across this mod and installed it. I immediately noticed that waypoints of completed contracts would no longer disappear after the task was complete, and I see no way to remove them manually, as they can't be deleted like custom waypoints.
Even worse is that these waypoints persist when loading a game, even though the game was saved without them. I tried saving, accepting a contract, then quick loading when I didn't like the positions of the waypoints (I did this in flight using the CapCom mod), and the waypoints stayed after load, even when the contract was declined. Repeating this generated even more identical waypoints on top of each other.
Fortunately, exiting the game entirely (not just to the main menu) does fix this, but it is an annoying workaround.
Is it possible there may be a mod conflict? I'm also using Contract Reward Modifier, Contracts Window +, and CapCom (access contracts in flight), but the problem only started when I added Waypoint Manager.