It does this on some of the waypoints, that are usually single but not all the time. At the moment I am going for Kataru in Zangarmarsh (Screen Shot added below) It shows the way point over the water when he is in the building but the waypoint moves toward where it should be when I fly close to the building, instead of being on the building no matter how far away I am from it. It doesn't go to the correct location until I am right on top of it. I flew around the building it went around two, and I went in the building it was still on the edge but as I moved toward the center it did too.
It maybe something to do with Carbonite, the Dugi Arrow can be funny like that sometime with carbonite because they have their own set of rules for their map. I would recommend you use the 'Use Carbonite arrow' option.
It still does it occasionally with that option Dugi. Close/Open the map usually helps.
Carbonite is having problems with node locations during routing too (not setting to the next one unless you pause if nodes are less than 100 or so meters apart) so I think they have changed something about the way they are doing positioning.