I've noticed the following issues with my game, granted I have a lot of downloads, but it is possible there are known fixes for these.
1. When selecting maps, the normal icons for Marine Mania and Extinct Animals do not show up.
2. The icon for the extinct status is missing
3. Placing a misty spring crashes the game
Sounds like you indeed have too much on your game, hence why it's having trouble loading original files.
Sorry, but right now I'm on my phone. I was able to resolve the misty springs bug but do any mods add their own conservation statuses? I found a few minor oddities that I was able to deal with by carefully pruning out the offending files. The missing extinct status icon is still kind of bugging me.
Looks like I could try Okeanos' Conservation Status mod, but I would need to locate it.