Thank you Jummivana. Here is how to reproduce the scenario in the first post of this thread.
Open dev mode and travel to: 34.243973, -116.781015 (The closest airport is L35)
You should see a little lake. Usually in real life (and in Bing imagery) this is a dry lake.
Surround the lake with a polygon
Select (Properties → Water → Exclude → Water), and the lake does not disappear like it used to. All that happened is one corner is gone:
Next to that is an even bigger dry lake. With this dry lake, instead of only excluding a corner, it keeps one corner and excludes (almost) everything else:
Near that is a wastewater plant. As you can see, only half the water is being excluded:
This is how my mod is supposed to look:
This is how it now looks:
How it’s supposed to look:
How it now looks:
How it’s supposed to look:
How it now looks:
Also, the water changes when moving up and down in altitude:
The examples in this post are related to this mod: