Been wondering if anyone else has been having some issues where the game seems to get confused as to where your engine is when doing shunting from the the head of the train. For example, I was recently playing with Thomas at Maithwaite Station in Free Roam. I was heading north to FFarquahar. During this point, I had uncoupled from the mail van I was pulling and ran around to the rear and coupled up to the van using Thomas' front coupling. I then shifted the train into the siding before reversing back onto the mainline. Once I was on the main, however, the game was still behaving as though the ail train was still part of my consist. As well, I became unable to set any new waypoints. The game would prompt "Go here", but the point wouldn't commit. It behaved as though I never set one. Has anyone else had this issue? I also ran into it when attempting to run around at Knapford with James.
I've encountered this several times when uncoupling from a train and wanting to head somewhere else with the locomotive while leaving the train behind. I've normally had to delete the detached train to be able to set a new destination for the engine again. Like in your case, it appears the game thinks the detached rolling stock are the train you're setting a path for rather than the locomotive you're driving.