Sadly, if the mission didn't count in your current achievement list, that means that the database is broken. So if you see a bugged achievement list, wait until the promised update comes.
I found that the bug is not for ALL achievements. Some still can be completed. Per example in my Aeria account the last interceptors wm in molikar counted for pirate but no for normal list, and resurrectors counted for normal but not for pirate, even when I did both in pirate mode a couple of times. In Solaria my Antares squad achievement counted only for 5 or 6 missions, even when I repeated all the missions in squad.
For me, the bug raised after the last Spaceball event. I think that the Spaceball achievements that counted separate solo, squad, pirate solo and pirate squad for same missions, broke the other achievements.