I have encountered two ships called Merchant of Sol, both of which act as one ship and are somehow overlayed, a command given to one is given to both. However, clicking on it a selection box appears to select between thet wo ships. They can be found in the Kennatar system in the attached save file.
I have uploaded the save with the filename taltamir 1.0.4.4 2010-04-30 Merged Ships Bug.rar
Now I remember that there was bug with merged planets in 1.03. I didnt find any thread about it (anyway I am lazy for long time search [8D]). I ordered constructor to build gas mine on gas giant through expansion planer and I noticed that in expansion planer were two identical planets marked as target for constructor. I check it and there were indeed two identical planets on same spot acting as one. I opened editor, deleted one and everything was alright. If it was mentioned somewhere else just ignore my post [:)].