(Running all of the ships at once) When the type B is selected, the game crashes. (this occurs because of this ---V )
The layouts of the rooms become intertwined, this is because the all of the ship files (for the weapon mounts and the one txt for rooms) are all named "myship".
(Running Type C alone) There is one room that's missing doors to enter it, this can become a huge problem when boarders decide to invade that room. (The room is right above the weapons room, and right next to the drone room)
The weapons system starts out at one, whereas you are unable to power up the Pegasus missiles, making the ship a sitting duck in fights (this also appears to be the same with the engines and shields, unless they are intentional.)
The repair and healing bombs seem to be a bit redundant, the healing bomb would make sense if there were no med-bay or if there were a teleporter. Repair bomb also seems to be slightly useless, considering you have an entire brigade of system repair drones to start off with.
(Running Type A alone) There is nothing really wrong with this ship type, it seems to be a slightly nerfed Kestrel A, but does offer the option to run slightly more powerful weapons early. Also, there is another room (technically two rooms, there's another room adjacent to the room without doors) crewmembers cannot enter.
(Running Type B alone) There is a glow to the engines room, but no one is actually able to man it. This ship type is extremely overpowered, the option to start off firing a volley of 8 total lasers is extremely powerful, the debuffed engines don't really make up for it. (I suggest to limit it down to 2 dual lasers, set the power down so you can only run two dual lasers.) The piloting room has no doors to it, leaving the pilot (and the very first new crew member) to be stuck inside. The engines on the ship graphic seems to be chopped off.
Type A Doorless rooms.
Type C Doorless room.
Type B unmannable engine room.
if so, go into blueprints.xml there should be <shipBlueprint name="PLAYER_SHIP_HARD_2" 
(Just to check, you did rename these files?)