The water on top the clouds looks like an issue with the order in which layers are being rendered. The same issue has been present with the fog surrounding a planet when in space. These are layers passed to the shader in the wrong order, resulting in something that requires to be on top, to show below instead, or vice versa.
The water at the horizon seems to me a somewhat different issue, although most likely still shader based. Water requires to render on top of land (of course), but it appears there is a range/distance involved where it stops to calculate if land is above water. Beyond this range/distance, it just renders water on top of land (cutout shader pass) regardless, all the way up to the level of the horizon. This is why you see some land above the horizon (right side of image), but water drawn over the land below the horizon (left side of image).
I have limited experience with shaders and the issues shown are likely more complicated than they may appear to be. I think the main issue could actually be performance. Sometimes you just have to take certain results for granted, where fixing an ‘issue’ could put an unwanted strain on our hardware. This is something I have started to notice ever since Atlas Rises and not just ‘shader’ side. I find it actually quite remarkable to see what HG has been able to pull off compared to the compromises involved.