Wasn't it just a bug of the game spawning Elerium if it had nothing else to spawn from your stores? (ie you have a clean base, so to populate the 2nd storey of your general stores, it takes Elerium since there's nothing else). At the end of the mission, you would then recover the Elerium as new Elerium while keeping the old one too.
I'm pretty sure you get absolutely no material from defending a base in OpenXCom.