If you use a "Set Editing Costs" module to disable the editing of objects, you will receive a message saying "Editing entities is not available" when you move waypoints. However, the waypoint being edited will still be moved regardless.
Presumably the message should not come up for waypoints, since (under circumstances where they can't be moved) they could just be deleted and remade in the desired location regardless.
Attached image shows the issue in action. You can't see my cursor but the waypoint is near the bottom of the image
This happens with deleting objects. If its not allowed, "Deleting entities is not available", but the object will still be deleted.
I thought that got fixed a while back? I definitely haven't experienced that problem in months
Edit: It's also not directly related to this really. That sounds as if the module isn't doing what it's supposed to, this is simply a failure to account for waypoints in the scripting.