That's a very strong version mismatch.
Xenonauts 1.65W is correct, that is the latest non-Community version of the game. But X:CE 0.25HF2 is a very old version from before some critical features, like the ability to combine several mods. So it shouldn't be expected to work.
You should clean up your installation, remove the X:CE and mods, and download a current version of X:CE from the forums. 0.34.1 is the current version and you can soon upgrade to 0.34.2.
The XNT/Xenophobia mods are also very old. You may find some info on the forums about how to run them on the current versions of the game, but I'm not sure if that's even possible anymore. If you want to play a big mod, you should play X-Division, which initially started as a continuation of XNT when XNT development stopped. However, X-Division is very different from the base game, so I would recommend playing the base X:CE at least once before diving into X-Division.