I was thinking more the power supply rails being a problem than the data lines. It would be nice to see a mock up schematic for those though I suppose.
As GremlinWrangler says, a common solution is to connect each power source through a diode, so there is no way for one to feedback into the other.
Re: data lines, yes you should take account of what voltages might appear on a pin of an unpowered chip, if there is a possibility of the other chip being powered. Usually the datasheet will tell you not to have a pin at greater voltage than some percentage of the input power to avoid damage. Or, if the pin effectively becomes a short to ground, it might damage the track to it.
Potential solutions may again involve diodes, or even just a small resistor, something just big enough to sink any power that would otherwise be a short. As I say, seeing the schematic would be useful.