To recreate, make a craft with multiple command pods and connect the section containing one command pod to the section containing the other command pod. Place (an) Ion Engine(s) on one section. Load into a sandbox and be in orbit. Activate the Ion Engine(s). Activate time warp. Watch as the two docked parts of your craft immediatly separate upon time warp activation and you either leave half your craft behind or crash into the other half. Be big mad. Get happy in the same pants you got mad in. Submit a bug report and call it a day.
