Comment by krisoft
I read and agree with all those options being possible. Except the "they may have had a batch of bad fuel". How would that work in your thinking? I can imagine a bad batch of fuel leading to engine damage or flameout and many other things, but it is hard for me to imagine how a bad batch would lead to not enough fuel remaining in the tank.
If you have more water in the fuel than you think you do (there always is some due to condensation in the tanks) then you might be able to reach your destination but you'll be burning more 'fuel' than your original estimate would have you believe because there is less power per unit weight of (contaminated) fuel.
This is fairly common in GA and there are cases where it has happened in scheduled flights as well. That's why fuel sampling is common practice.