Are you playing a custom map, or random? Because I went through each stamp by hand and removed ALL rivers that should not be rivers, and I checked my stamp, those spots shouldn't be rivers by the stamp.
I do know they are in FE because they haven't fixed them yet. I also, know they exist in the custom maps because they haven't taken my fixes for that yet either.
The other invisible river tile (not the circled ones) happens when another stamp overlaps the river. It removes some of the river data, but not all of it and one ends up with these invisible rivers from time to time. The other stamp that does this is Curgens Tomb.