Sorry, I forgot to mention that I am running the game modded, and it may be due to that, I'll try to see if I can replicate the results with the game unmodded.

edit: Managed to replicate the results on an unmodded game, It seems to come into effect when more than 20 planes are placed down, and when you switch between the 3d editing mode and the singleplayer scenario mode a few times.

I have the same problem, running the game modded, placed down a 2 Hematt trucks and grouped them together, then placed a support waypoint. The group leader remained stationary in the editor but the second truck was driven to the waypoint by the ai in the 3d editor, also leaving behing the x,y, and z arrows behind