Hey there,
Despite seeking help for this issue I couldn't fix it before 2.1, train connectors are incredibly and fickle on a 1x1 entity. Increasing connector tolerance helped a little but messed up the graphics in other situations.
With 2.1, we're getting new train connector graphics and logic and the connections now always align when the wagon is next to the pump! In addition, you may also connect your plasma wagons on diagonal and curved rails.
Thanks a lot for the report!