One wonders how often this might happen in the development world.
Check out the picture of each game's topography as first shown at GamePressure ; as you can see, the two maps aren't that much different. Later, a source close to Ubisoft supposedly confirmed to Kotaku that the designers used FC4's heightmaps "as a basis" for the new entry.
But before you flip out, we should remind you that Primal don't look like FC4; it's not like you'll be playing it and going, "damn, I've played on this map before." You're in 10,000 BC for one thing, and the gameplay is distinctly different, so don't worry about a recycled experience. It's just that they obviously used a preexisting tool, which probably isn't uncommon within other franchises.
Related Game(s): Far Cry Primal