My friend used a mobile app where he could log in and chat in the server. The app allows him to send emoji characters, but when I receive them in my Minecraft (the game) client, an empty message appears after his username in chat, like sending a whitespace-character in some chat programms.

I guess either the server or the client should check whether or not the character is render-able with the current font. If it is not; don't display it (and maybe let his client know his message was invalid as well?)

(edit) I guess it's this app he used:
http://www.minecraftforum.net/forums/mapping-and-modding/minecraft-tools/1264022-android-minecraft-chat-app