When I was exploring my Mesa world this chunk appeared... It was filled with water for about 10 of height. Water is on normal sea level.
seed: 774205031375500968, customized: Biome: Mesa Plateau F

Edit: I though it's connected to the Mineshaft but it was near it and looked fine.

Edit v2: seems affecting some other chunks, so it is not "so" random.
Same world, attatched new image.