They are confusing the concepts of an app level vs OS level mute. If the app itself paints a mute button, of course there's no guarantee that it will do what it says. You have to trust the developers at their word, that they are actually ditching the audio feed coming into their application. Some apps even use the audio to provide useful functionality (like a "you are speaking while muted" notification). If you are really concerned about it, mute the app from system controls instead.