I've also had the experience several times that when I've got something running, like the Fruit Changer, and I switch to another Chrome tab, when I switch back the thing I'd had running is in some infinite loop, making no progress, not using any raw materials, etc. I can't click on the red X to stop it, nor make it cease in any way other than to restart.
I've managed to reproduce this, though I can't really track down the precise cause either. I've filed a bug and we'll look into possible sources for this kind of thing.