In the attached save double-clicking on an uninstalled ship landing beacon selects only 2 out of 4 beacons.
This may have something to do with the fact that two of them were installed and then uninstalled after all four were brought in by caravan from the deserter quest.
The save was produced with a few QoL mods but I can reproduce the bug when the same save is loaded without mods.
THanks for the bug report. I wasn't able to reproduce this on a fully unmodded playthrough, unfortunately. While I was able to get it on your save stripped of mods, unfortunately removing mods can sometimes keep bugs that were happening from the mods. I will add this to a list of bugs to look out for while testing though, in case it comes up for me.