That typically happens to raised terrain that is overwritten by water. Like if you have a raised area then use a deep water brush over it without lowering, or vice versa, you may have to raise it to shallow and lower the shallow. If its really stubborn you may have to follow it to the source of the problem.
Sometimes you can cheat it if the brush size is larger than the area you are overwritting. Basically, what you are seeing is the edge of an area that was outside of the brush when you used deep water.
try using the lower brush across that area then deep water over it. Or lower, then shallow and deep over the shallow.
It's hard to explain, but my map is all deep water so Ive been there. hope this made sense | 
