This is basically true, and as designed! To elaborate: once your vessel's parts have all been destroyed except for the main pod, the pod switches into a critical defense mode. Your pod will defend itself by consuming any crystals you have left in order to power its shields. At this point, you should definitely be retreating away from enemy attacks. If you fail to escape before all of your crystals are depleted, the pod will emergency warp back to the trading post so that it does not get destroyed.