When you assign a new fleet member that's located in a different sector than of your flag ship, it will align to the flag ship with the correct local sector coordinates...but in the wrong sector ^^
The ship I assigned (targeted) is now aligned, but in the wrong sector (2000 meters + 300 meters of sector overlap)
I've also seen something similar happen in the past build when crossing a sector with your flagship, most if not all of your fleet members would not align properly then but that might have been resolved. I see something else happen but that might be unrelated.