This has been a problem with every single version of GC. Autosaves are taken after the ships are produced, but before they are launched. So if you load an autosave after a crash, you have to go examine each and every world/shipyard to see if you had produced a ship that you wanted to be launched, and eject it yourself. In earlier versions it would also leave planets that had finished a project idle, but at least in GC3 idle planets are brought to your attention.
Several of us suggested for GC1 and GC2 that the autosave be taken at the time the turn button was pressed, before any planetary or ship production, but this was never implemented.