I've been having the same issue. Followed coordinates, hopped out, and my EVA did nothing. I just realized that once I hopped out the waypoint seems to have shifted. 63.1km and far from the icon on the map. So I flew to the new coordinates. It's worth noting that when the waypoint shifted, the navball icon didn't show up anymore. Once there, I hopped out and the waypoint shifted another 63.1km away. So got back in my plane and took off for the new waypoint. This time around, the navball icon showed up and I believe it was in the direction of the original waypoint. Unfortunately, upon hitting 4x time (I was getting impatient) my plane flew apart. v 1.0.2.842 In this image, I've arrived at the second waypoint after the first one shifted. I hopped out and it seems the waypoint is still far away. The new waypoint is just visible over the wing on the right.
