If there's any sort of module (battery, solar panels, etc) that goes between two habitat modules, then they all get considered as being the same "base" that shares a single supply of oxygen etc. If your bases are way far apart, and nothing is connecting them, and they're still sharing oxygen levels, that's definitely a bug.
Unpowered tiles flickering: I haven't seen this yet. Any chance you could post a screenshot of the base? Is it huge? You're not just talking about the lightning icon on them I'm assuming but like... the color flashing constantly or something? O_o;