Is there a way to remove these black squares on the player's face?

Issue:
it bothers me a lot
Game:
Pokemon X

In order for us to provide better support, we need to see the log generated by Citra. This guide will walk you through how you can obtain the log file: How to Upload the Log File.

No and it’s probably not going to be fixed, read this

You might ask in a Pokemon hacking community if it would be possible to “fix” this by modding the game.