I've encountered this scenario when trying to prepare for my 3rd ship, I got one for free because of a bug. The 4th pic (pre-bug) shows I have only 2 ships, and I am building a 3rd cargo dock(4 module), for when I repair the 3rd ship. Pics 1, 2 and 3 are all after the bug happened. Pic 3 shows the main shipyard with resource still being accumulated to repair ship 3. This ship 3 is shown in the world map on pic 2, and it hasn't been repaired. Pic 1 shows all 3 ships with the indication up there 2/3 ships (available repaired/discovered). What happened was, When I upgraded one of the 2 module docks , when that 2 module ship took off to main map to return as a 4 module ship to that dock, two ships returned, and the only way to prevent this was to delete the 3rd dock (the 4 module one), prior to the upgrade on the existing oil dock (2 module) that I wanted to upgrade. It is worth noticing that when doing this and following with normal game playthrough, I then built a 3rd dock again (after deleting it for the upgrade of one of the previous docks), and this 3rd ghost ship didn't appear. Only appeared after I finished repairing it with resources, when it came and finally the top portion of the screen showed 3/3 ships (available repaired/discovered). I have the save game prior to this happening and can replicate if needed.
My regards
Z
