It's simple bug and it makes submarines useless:
You choose one of your naval units (even embarked ones). Click "M" and besides the unit movement area you see some tiles on the sea (even in the for of war) marked. There are submarines in this tiles. Then you simply move near to one of this tiles and see the sub.
You choose one of your naval units (even embarked ones). Click "M" and besides the unit movement area you see some tiles on the sea (even in the for of war) marked. There are submarines in this tiles. Then you simply move near to one of this tiles and see the sub.