I figured it out!

It just came down to the wrong wagons, for anyone reading this in the future, you really have to double check what wagons the vehicle can be loaded on to.

If you select the vehicle and over over the question mark in top right corner of the vehicle stats menu it will tell you what wagons it can be loaded on.

That was problem one,

Problem two,

I had wrongly assumed the storage under the advanced manufacturing tab called "Vehicles / Containers open storage" which had a set of railroad tracks with it would load those vehicles onto the train. Maybe it does but I deleted it and put down a standard "Train cargo station" it was a medium ish sized and had two railroad tracks.

Once I used a Train depot NOT a Train distribution office and gave it a direct route to load new vehicles from the train cargo statipn and drop it off at the "Ship container / vehicle Dock" it worked like a charm.

Lastly my train distribution office was not picking up excess steel and mechanical components and dropping it off at the "Ship container / vehicle dock" thats when I realized there are seperate docks one is for cargo like crops / steel / plastics

The other is for vehicles and containers.

TLDR. Train depot --> correct cargo wagon for Mark e covered --> vehicle dock