Compare the waveforms on the left and right tracks. If one is going up when the other is going down you have either a polarity or phase problem. If it is polarity (waves in mirror image) you can flip either the left or right (obviously not both!) using either the Trim plug-in or the Audiosuite Invert.

If it is a phase problem, one side is shifted either a little earlier or later than the other. In which case nudging one of them forward or back so that the peaks and valleys line up will fix it. In a final mix of a multitrack session, though, it is likely that any phase problems were only on some of the tracks, not all, that were being mixed. This makes it more difficult to deal with, because by nudging one side of the stereo mix, you may bring one element back into phase while throwing off something else. Fixing it may require remixing.