Do those patches move or vanish if you change the time of day? If so, they might be terrain shadows. No and they are only on certain parts of the layout and depending on if you rotate it, it looks like water which I have not put any in.
OK, what happens if you copy and paste a bit of “good” terrain (texture only) onto one of those dark patches? If it removes the patch it might suggest they are something to do with the ground texture.
What else have you tried and what were the results?
if it is anything like Trainz+ , it could be the water layer. the water layer is always there, you just have to make it lower , so that it does not show where you do not want it too.
goto layers and change the level of the water layer.