If you leave the Battleship's sections after getting the second blueprint, it will let you collect it again

It doesn't always let you do this, and I'm not sure if it only works in certain sections, but sometimes after fighting a section's boss, the next room will have the final blueprint for the area (as well as other items) along with a choice to continue or leave. Choosing to continue gives a brief message and you leave anyway, but if you pick leave before seeing this message, the game doesn't consider the section beaten. As a result, you can go and do it again. Doing this can get you multiple copies of blueprints. Sometimes the boss isn't even there on subsequent visits, but sometimes it does reappear (I think, not properly tested this).

Not sure how to fix it other than to make sure it doesn't give a blueprint you already have, and to not let you simply leave on the screen right before the forced leave message.