Yea, did you clone those tracks that cannot be heard? Or did you record those tracks at the same time with different microphones?
If you used mics when recording, Phase is something you need to take into account and fix at the recording stage when using mics.
If you cloned the tracks, then you need to nudge them back or forward. But its always best to record different takes of the same sound instead of cloning the tracks. You get way better results and phase will never be an issue
CJ