The mod endeavours to be compatible but you need to understand this mod uses LUA scripting. This means if you use other buggy mods with LUA scripting and they cause a script break, then this mod will be affected. In a worst case scenario, this can render an objective uncompletable, which of course is quite frustrating. So the more mods you run that use LUA scripting, the higher your chance of having this happen to you.

So what to do about this? First, keep your mod list trim to minimise the chances of this happening. If you're playing a Queek campaign, then don't leave your Nakai Overhaul mod enabled - you're just taking an unnecessary risk for no reason. Second, enable Context Viewer in the main menu under mod settings. This warns you when a script break has occurred by a giant flashing red X in the top right of the screen. Then you know to reload your save before you continue playing.

Additionally, if you run the Script Debug mod, it generates error logs in your game directory after every game session. So when a script break occurs, you can open this log in Notepad and search it for 'error' and it will tell you precisely which one of your mods caused the script break.