I get that message too. I am not sure why or how to extract any logs that may prove helpful in figuring out why it does that.

Today when I loaded into my saved game I got the message: "Mod-related problem detected in the game logic. Try disabling the mods in case of unexpected game behavior. Mod Flagged: Indoor Polymer Factory"

I disabled the mod, restarted the game, opened my save game and resaved it, exited back to main menu and enabled the mod. After restarting the game again and loading my save game I got this message again. I had no issues with it yesterday.