(As it pertains to my '09 Dyna FXDL)
The system relay supplies power to:
1) Fuel injectors
2) Ignition coil
3) Fuel Pump.
Before the engine is started, when the RUN switch is set to the run position the System relay is picked for 4 seconds and then de-energizes. When the starter button is hit and a crank signal is sent the the ECM the relay once again is picked and is held in as long as the engine is running and a crank signal is being generated. If the crank signal should cease, the relay will de-energize in order to kill engine and stop fuel pump pressure. (safety feature).
Remember, the crank sensor is self contained and needs no external power supply for it to generate an output.
In your case I would say the ECM saw that the points were closed when they should not have been. Check your system relay using a meter and a battery. It could have also been a timing event fluke. Erase the code and see if it re-appears.