I think i can explain you when this bug take place. When server runout of memory and crashs he saves a backup savegame with a location and all data of player ship and when i try to load savegame server load backup and actualy save. so when loaded we have two ships: actualy saved ship and ship from backup. they placed on different system sectors of map. Also we with my friend repeat whis bug for few times.
in server and client log there no interesting no errors or other, but if you needed i can send it to you. they just too large for attachment to post, i'll left links to them
https://dl.dropboxusercontent.com/u/22981762/clientlog.txt
https://dl.dropboxusercontent.com/u/22981762/serverlog.txt
P.S. we with my friend also crash game when mod turrets with increasing firerate. so when too much shots fly ower space game crash with runout of memory. thats how we duplicate ships fitst time. also i think that time of crash important. so if game crash's when you in one system spend alot of time ship don't duplicate and if crash was when you travel one or more systems it can be duplicated in start of travel(where was last save) system and in exacly in system where you are.