I've been using this for some time, and few oddities seem to pop up every few games. Worth nothing that I'm using it quite liberally, sprinkling extra wonders, resources and even features a bit on map.
Dummy luxuries. Occassionally I get a luxury that increases the tile yield, I can improve it, but it doesn't actually work as luxury resource-doesn't show as happiness increase, can't trade it away but can still trade it from AI like I don't own it.
Inexistant natural wonders. The popup when discovering NW says there are still wonders left to find, CS ask me to find them, but there are none-I have entire map explored.
One game, I used the features to expand coastal area around my starting position (used fill with water to land turned off, so it just overwrote all ocean tiles), and one tile was unworkable and borders couldn't expand there (not even with buy) despite it being coast, and my galleases could go there.
I'll try to find some related saves if you want, but I doubt there are any right now.
Anyway, speaking about the coasts...do you think you could make an option to expand coastal areas to 2 or 3 tiles width? It would be really great, with one tile coasts naval combat and exploration before Caravels and Frigates is really not fun.
Oh, one more thing. Sprinkling some strategic resources around often result in those being just 1 in quantity.