Are you 100% sure it wasn't just 2 copies of the same print?
I already had 2 blueprints (before the lvl 4 was finished). 1BP for lvl 3 and 1BP for lvl 2. Unluckilly I got the same BP, so I still had only 1 unique BP. After 4th lvl completion I logged in and saw a reward welcome dialog. It got me my 30FP, some medals and there was only 1 blueprint. Obviously my first thought was that I got only 1 unique (but 2 as a quantity), but when I went to observatory window i GB section, I've noticed I got only 1 BP and I have now 3 in total
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I don't know if it was innogame developers that fixed it (I also reported this issue with innogame support tool), but now that I went to the observatory in GB section I noticed I've got brand new blueprint and have 4 in total. Maybe it just fixed itself. As far as I'm concerned, Im satisifed.