It's probably made even more of a problem for the Normandy expedition because of the incentive to disconnect and play offline. Trying to find uncharted systems is a chore if you don't.
So let's say you just forgot to reconnect before creating your base, of course the game won't find any overlap.
The game should check overlapping again for upload, not just creation.
Isn't that the wreck of a port with botched controls, horribly misshapen characters and "enhanced" textures that misspelled environmental text everywhere? Occasionally completely missing jokes by doing so?
Was it supposed to be fixed in any way at some point?