So I like to play as a custom synthetic race (Insert formalities here)
In a nutshell the CPU-MS, that is the default medium missile systems ship, does not appear to be a medium sized ship. When you unlock large hulls you can build it but it is a large ship and a clone of the DPU-MS ship (The large missile systems ship), albeit with a bit of a different look. This is rather annoying if you like missile ships.
Anywho that's the bug, thanks for the help.