Audio Issues on recording playback

[suburbanwitch]

When recording for podcasting I notice an issue that when one person talks, any 'talking over' eachother, or grunts of agreement from the second speaker cut out the main talker or just get muted automatically and I don't know how to stop it. 
I always use separate audio files for myself and my guests, but even if I cut out their 'cough' or weird sound from their audio, it has still muted or distorted the sound on my own audio recording. 

This is a frequent issue that I've been having and I'm unsure how to avoid it. It obviously makes laughing together over a funny joke sound wacko weird and not nice and I seriously hate having to deal with this issue.