I does not happens all the time, but it has appeared at least twice. there are some weird symbols overlays that appears on the map only during gameplay (they are not in the map editor). I was wondering if it was a feature. Here is a shot:

As you can see, there is some dark stains in the middle of the dessert, and on the grasslands on the left, there are some wavy and curly shapes drawn in light yellow.
Take note that I have been hacking the XML, so I might be the problem. But I have not see these shapes anywhere else. Maybe there are cloud effects in the defined CoreEnvironment XML?