I haven't used Train Simulator classic for quite a long time and I have got back to it recently. What on earth has happened to it? We cannot couple rolling stock together anymore! When you place a train into a scenario for a route, the coaches are heard clinking as you TRY to place them on the track - only for other coaches to disappear or that they don't couple together making a large gap between the train. This has never happened before ever!
First check in your Settings - Gameplay that Allow All Coupling is ticked. Maybe you are trying to fit a coach where there is not enough space in the train? Move the loco forward slightly and the couple the stock.
It appears that you have some assets that are missing .Geo files, other dependencies, or corrupted files. This can cause "invisible" rolling stock "wagons" or only couplers to appear in some cases when placed in the editor. You might try a file verify to see if this helps. You did not say if this happens with everything or only to certain items.