If the ship uses, say 4% of its fuel in a 5 day increment. And at the end of the previous increment it had 50.1% or more fuel, then it would continue on its orders. At the next 5 day increment, it is under 50% fuel (46.1% to 49.9%) and the conditional order takes effect.
This is how that happens. Conditionals are not interrupts.
This "feature" gets more egregious when you are running longer increments. In shorter ones it rarely happens.