Seas have internal waves just like they have surface waves.
Internal waves are gravity waves that oscillate within a fluid medium, rather than on its surface. To exist, the fluid must be stratified: the density must decrease continuously or discontinuously with depth/height due to changes, for example, in temperature and/or salinity.
Wikipedia, Internal Wave, 2018
The internal waves travel more slowly than surface waves of similar amplitude because the difference in density between two water masses is much less than it is between air and water. The internal waves typically have wavelengths from hundreds of meters to tens of kilometers and have periods from several minutes to several hours. Internal waves are trapped in the pycnocline of stratified oceans.
Journal of Coastal Research, Remote sensing of ocean internal waves: an overview. KLEMAS, V., 2012. 28(3), 540-546. West Palm Beach (Florida), ISSN 0749-0208. .
It is easier for internal waves to travel between layers of different densities at the pycnocline. In open oceans this is much deeper than the photic zone. This means that those waves travel in complete darkness.
The Quran talked about those internal waves long before it was discovered:
(Quran 24.40) Or like the depths of darkness in a vast deep ocean, overwhelmed with waves topped by waves, topped by clouds: depths of darkness, one above another: if a man stretches out his hand, he will not see it! If Allah does not give light to a person he will not have light!
"Waves topped by waves, topped by clouds" are internal waves, surface waves then clouds. In deep oceans you cannot see your hand because there is no light down there. So in deep oceans those internal waves travel in darkness. No mistakes in the Quran.
How could an illiterate man who lived 1400 years ago have known that seas have internal waves? How could he have known that they travel in darkness?