I have a slightly different problem. I completed all three tasks for Javaal Fleet Action mastery, and all three are checked off in my legacy log, but the status is still listed as incomplete and I have not been awarded the achievement points. The progress bar on the achievement is full, all objectives are green & checked, but the status text at the bottom is incomplete and I only have 10/15 points for the Javaal Fleet Action.
Incidentally the achievement was left in my tracker (title only) but I was able to untrack it since it was marked incomplete.
I just completed all the bonus objectives for Javaal Fleet Action Mastery and have the same issue. The tracker shows only the achievement title, the progress bar is full, the individual requirements are marked off, but the status is incomplete in the achievement details. I never received the pop up notification and the status bar for the Javaal Fleet Action subsection is showing 10/15.