I am try to download patches and mods (Because the AI is awful) but I am having problems updating the game with the patches I require. It says something about a incompatible version or something.

http://www.tauniverse.com/forum/showthread.php?t=39834

The game is already patched to 3.1c by GOG. So you don't need to apply the 3.1c patch, because you already have it.

The 3.1c patch will give the error you are describing if you try to apply it to a TA install that is already at 3.1C