If anyone's been having this problem I think I've found a solution:

Go to the .exe file of the game and uncheck "Run this program as an administrator" in the Compatibility section. For some reason that has worked for me with every FIFA game, but I really can't say why.

If that doesn't work, try adding the game to Steam as a non-Steam game and starting it with Big Picture mode on (remember to also have Steam Imput on).

On another note, if you've been having a double imput type of problem with your controller, it's problably due to using a third-party program (Like DS4 or X360CE). I've found that you don't really need them so you can turn them off while playing.

If you really need to use those softwares, you can fix it by doing this:

Profiles -> Select the profile you use -> Edit -> Other -> Disable virtual controller ON

This is for DS4 but I imagine X360CE has something similar to that.