The latest core should be targetting the underwater biome; if your version had water, then it seems like it was an older version.
The spawner in the latest core is set to about 0.01, I think. If you had a much higher probability count, it probably laid a lot of spawners. it draws from the entity groups AnimalSwiming. From what you've said, they spawned a lot, so the random number generator probably didn't get a chance to refresh and pick another fish type.