So I'm playing through a game as Sophons, and I've been slugging it out with the Cravers for quite some time now. They've got some nasty missile dreadnoughts, but if my laser battleships can cut them to ribbons before they can fire, that should be no problem, right? Except that, invariably, even in a case of one dreadnought versus nine battleships, an exchange in which the dreadnought is vaporized instantly in the initial exchange of fire, I am still absolutely guaranteed to lose one battleship. It'll often explode at the tail end of the victory screen, with no sign of any enemy fire anywhere remotely nearby. Is there some sort of a hidden bonus to dreadnoughts that they can't get wiped out without inflicting at least one counter-casualty if you have dreads or something? I've been fighting this war long enough to see this repeat many, many times, and it's starting to get weird.

This is very commonly reported. It seems that their missiles are fired early in the first round. But, they are invisible due to a graphics bug. Then they hit you during the victory screen. Please see the resources in my sig for more information.