Thanks for reporting! When you buy a ship the game automatically sells your existing ship and applies that credit towards the new ship. The ship you start with in the game is the Fork so you are actually selling your old Fork and buying a new one, losing the difference each time :(
As you noticed, the real bug here is that I'm not making it clear what your current ship is (which also is tough when buying weapons).
I hope to overhaul all of the game UI to be far more functional based on player feedback, as well as prettier to fit into the game better. The UI is "programmer art" at the moment and is missing some important components.