Spurius
I finally decided to have a look at this and see what was happening. Also downloaded your big map to see if it was having the same problems on the Cornwall bit and it was. Switching heights to 1,1,1 reduces the size of the problem square but doesn't remove it.
The simple solution for getting rid of it is to change the sea pixels to be a lower blue value eg 0,0,240 seemed pretty good although for the 2,2,2 issue 0,0,249 or below seemed to resolve it (Note I only did this for the problem squares not all - I don't know if there are any side effects to that or not).
Also spotted that the pixels where sea pushes into land ie the top right pixel being land and the lower left being sea it is best NOT to use heights 1,1,1 and increase to 2,2,2 - this will then stop the reverse happening i.e. an edge of sea appearing in the land.
Thumbnail below (sorry its quite big) shows Dee estuary left side corrected, right sides top shows indentation of sea (corrected afterwards as explained above). Mersey estuary on right side hasn't been corrected and so shows both problems.