I know this has been reported before, but I have a save where the problem is repeatable.
When my survey ship investigated a Ship Graveyard, I did not get a notice that it was defended. I was stuck with fighting the pirates. Wow! They are much more powerful now. My survey ship destroyed one before being destroyed. I used Alt-Tab to leave the game and get to my GalCiv3 directory. I made a copy of the autosave, then went back to the game. I loaded the autosave copy and investigated the Ship Graveyard again. I still did not get a notice, had to fight and destroyed two pirate ships before being destroyed. I reloaded the autosave copy and investigated the Ship Graveyard for the third time. There was still no notification, and I lost again.
After today's video stream, I ran GC3 again, loaded the save, investigated again and got the same result again.
Save and other information submitted on Ticket #EXI-284-57864.