MacBook Muted, some applications still provide sound
The most likely explanation for this is that you have multiple sound output devices. When you mute, only the current output devices is muted — the rest are not.

The next time you hear a sound when you think you shouldn't, go to Sound Preferences > Output and check your Output devices one by one. It's almost certain that at least one of them isn't muted (a headset, for example), and that's how you're hearing the mystery sound.