3DSTool works better for this.
Make sure the CIA is decrypted first. You can use Decrypt9 to decrypt it.
Code:
ctrtool.exe --content=Content Game.cia
3dstool.exe -xvtf cxi Content.0000.* --header NCCH.Header --exh DecryptedExHeader.bin --exefs DecryptedExeFS.bin --romfs DecryptedRomFS.bin --logo Logo.bcma.LZ --plain PlainRGN.bin
3dstool.exe -xvtf exefs DecryptedExeFS.bin --exefs-dir ExtractedExeFS --header ExeFS.Header
3dstool.exe -xvtf romfs DecryptedRomFS.bin --romfs-dir ExtractedRomFS
That will extract all the contents of Game.cia including unpacking the ExeFS/RomFS.