I can only reproduce this by placing landfill into deepwater first and then filling in some water right next to the land fill with normal water. There is graphics issue here, if just a single row next to a row of land is normal water and the rest is deep water, you won't see the normal water. At some point when I was trying to fix this, the following happened: https://i.imgur.com/BcDe63P.png - this shows the tile setup I'm talking about, but without graphics magic. I dont know of a nice way to fix this honestly.
There is an additional issue with the smoothing the game applies to collision near water right now. Even without the mod it is possible to stand on a tile which is technically water currently. With this mod it somehow becomes worse and you can stand on the entirety of a tile which is technically deep water, if enough of the surroundings are normal water.
I'm keeping an eye out for this, but just don't know of a way to fix this right now. When you're playing, you can fix this with an additional row of landfill I guess.