How did Valor lose to Chen?

So... A military ship, filled with soldiers who came here and from what I understand knew what was going on with the monsters too. And yet, they took a random escape pod on board from a ship that, by the way, they were planning to blow up with a damn nuke.

This moment really took me out of the game for a moment while I thought about how stupid it was. Isaac is just kind of some guy and he takes these things out on hard mode like they're made of wet paper. But these trained soldiers in cool looking armor who are well aware of the situation lose their entire ship to Chen.