For once, they get spawned in river biomes, which triggers the real problem.
On generation, they carve out a large block and just fill it with water:

0.0.13beta on 1.10.2

I've never seen that in vanilla, probably because I've never seen so large rivers. To bad, but there is a config option to disable them. #worksforme

This is actually vanilla. They can occur in big rivers too. I'm actually using exactly the same generation as vanilla does so I think you just got unlucky. I can see if I can add an option to try to reduce them though