I wouldn't call it a bug, but more like the Portals doing what they were programmed to do. If you put one on top of the other, different devices will probably make the calculations differently on which Portal to listen to. Also it could be that, as you mention, you get stuck in a permanent loop between them.
It seems that the game is not able to scale to the correct proportions. I think it should automatically go Landscape, but are you using the iPod on Portrait for browser and then switching to the game to Landscape?