Regarding fuelling - is it like a petrol station pump, where the filler clicks off when the back-pressure indicates that the tank is (almost) full, or more like an airliner where a specific quantity of fuel is programmed into the dispenser?
The auto shut-off mechanism never worked very well with my 2008 Prius. I found it frequently cut off way before the tank was actually full, when holding the nozzle in the normal position so that the hose runs vertically up to the nozzle. I found that rotating 90°, so that the hose ran from the back of the car towards the nozzle, was more reliable. (Maybe because that model was a 'world car' designed primarily for the North American market?)
I'd assume that it's an automatic thing. I wouldn't like to be there holding the lever for 1000 litres or more, it's bad enough for 45. (Though I imagine the flow rate is much higher!)
If instead it's a specific quantity of fuel to load, someone has to measure the current level and work out what quantity is then needed. Not too difficult maths, but you need a good gauge to see the current level and an accurate knowledge of the capacity. If the gauges aren't clear or accurate, under-fuelling could well occur.
It also doesn't sound like the timetable allowed much time for refuelling, so mistakes could happen under time pressure. Errors usually have systemic reasons, they're not just down to one individual making a mistake.
I'm reminded of Air Canada's "Gimli Glider", where a Boeing 767 ran out of fuel mid-air due to repeated errors in calculating the necessary refill quantity. Although train fitters shouldn't have to deal with allowing for the density of the fuel!
I suppose in both cases, you would want a back-stop using the other system (quantity or shut off) to prevent possible spillage due to over-filling. In the case of a calculated quantity, in case of a miscalculation/misreading leading to an overfill; in case of an auto-stop, in case the mechanism fails to operate.