Audio channels within a mix are audibly out of phase with one another.
Phasing can usually occur when sync between audio channels is slightly out.
Bring your audio into an editor and view the waveforms for all the audio channels.
For 5.1 audio start to preview the front left and right channels to verify they are ok. If these are good enable the center channel, then the LFE, left surround and right surround, stopping at any point as soon as you hear the phasing issue. Adjust the offset of the audio channel you enabled when the issue presented itself by moving the audio backwards or forwards a frame or two. Does the issue improve? Refine the offset until you are happy you have removed the phasing.
For stereo audio it's possible the issue is baked into mix if it was created by folding down the 5.1 audio. However try the same process and see if you can remove the issue by adjusting the sync of the left/right channel.
You will want to perform this fix in a dedicated digital audio tool (such as ProTools, Pyramix or Soundtrack Pro) as it will allow you to make more refined adjustments (down to the sample).