This means that the two separate rocks were once part of one piece of rock. These layers got separated most probably by continental drift as a result of tectonic plate movements. An example of such a fossil is the Mesosaurus, a freshwater crocodile-like reptile, that is found in Southern Africa and Eastern South America continents- that means they were once one land mass.
The environment in these two separate layers would most likely be different. As the layers drift apart from each other , they drift across latitudes that are determinants of climate in a region. Therefore, even the organisms in these two rock layers will evolve differently (even though they will share a common ancestor) in adaptation to respective environments – this is called allopatric speciation.