I ran into a bug twice yesterday under similar circumstances in the same game of Gal Civ 2.
After upgrading (again, this happened twice with two different hulls) a vessel class and applying the upgrade to all such vessels in the field, a few turns later, presumably when all upgrades completed, every single shipyard I had started building the new class of vessel. If not for my roommate (beta/gamma tester Vinco) telling me how to stop it easily, I'd not know how to shut them all off.
Am not aware of any other circumstances leading to this malfunction.
-Dem