I have only noticed this recently, as I don't use Modern Apps very much anyway, but when I close Modern Apps, they remain in the left hand App Switcher list.
I have "Keep closed applications in the Windows 8 left hand app switcher list" under Advanced options unticked.
I am using Windows 8.1 64-bit and ModernMix v1.12.
Edit: It seems to be working correctly now after a reboot.