I wonder if it has to do with "africa" originally being in the "center" of pangea. The gators may have been located closer to the "coastal" areas of pangea and therefore "separated" when the split occurred.
That could be true, but it doesn´t explain how the crocodilians made it there. On the other hand africa has just few crocodilian species. The nile croc is very dominant.
Just throwing out ideas....Maybe they were specifically placed in the areas they currently live in, on purpose, to provide counter points to stupid theories.......