After some testing I found that Alien Biomes is not the cause of this directly. The shallow water tiles are not put in the game by normal map generation but it looks like Alien Biomes will use them, however they are vanilla tiles so I would call this a bug with the vanilla tile. I was able to work around the problem by just using the /editor command to swap those tiles out for normal deep water, and then land fill that. Or you could change it to land tiles and skip the land filling part entirely. Anyway, the last thread got locked from the mod author pointing out that all tiles added from the mod can be land filled, which is true, the one that can't was not their creation and is an apparent buggy vanilla tile just being used.