Ooh, I love the chance to retell this story.
Homeworld 1. The Cathedral of Kadesh. I had 15 captured Multi-Beam Frigates, and decided I'd send them all out against the last Kadeshi Needleship (the big needle-shaped mothership/carrier thingy). Once they got in range, I ordered them all to attack at once, figuring it would die incredibly quickly - but I'd neglected to factor in the MBFs' momentum, which kept them going for quite a while as they tried to align up correctly. Meanwhile, the Needleship turned round and started to try and ram the frigates (as it often does, being shaped like a baseball bat).
What then happened was, the MBFs began to phase through the Needleship, just spinning wildly into one side and coming out the other. It didn't take long for the game to realise that this should not be fucking happening, so it promptly fixed the glitch and made the Needleship material again. The problem was, several MBFs had been inside it when this happened.
They were never seen or heard from again. I like to think they remained trapped in there until the Needleship spectacularly blew up.
Oh, and one happened to my friend. Playing the latest Assassin's Creed, and he was trying to get onto a horse... but the horse was next to a tree, and something went wrong with the collision engine. My friend's outraged cry of "WHAT. I'M IN A TREE" remains my favourite thing he's ever said (aside from "History is written by people who can write").