Battlestation: Harbinger now named Battlevoid: Harbinger.

They are quite rare. When you look at the Alien ships in the start menu, the corresponding ships on the battlefield drop them when you destroy them. But they have a drop %, meaning they won't always drop.

And since the ships are more powerful you must get to map 3 and 4 to have better chances of encountering them. Happy hunting

Oh, and when a blue print is collected it is show with the same red alert text messaging as "enemy ship present" and the like. You can also scroll the start menu list and see how many you still need to find for each ship.