Got the save, thank you! Taking a look, hmm. You don't have the "Phantom" blueprint learned, so I suspect the blueprint you got was a different one. The entity that the Phantom blueprint was supposed to be on was a derelict ship, and it looks like that was salvaged, hmm. The only thing that comes to mind as a possibility is if you somehow missed it, and it ended up in some cargo pods that eventually went away.
Well, either that or somehow the game gave you the wrong blueprint from the derelict ship. Looking at the code, it's hard to see how there would be a mismatch between that and what the intel tells you the blueprint is, but it's possible. I'll keep an eye out!