This is going to sound silly but I'll bet money that it is the problem and the fix. Problem: thud in the rear end, not always but sometimes.
Cure: your passenger side window sometimes, or in my case, always goes up too high. Poor calibration. All I do is open it a tad, not enough to let any air in but just enough so that it clears the weather stripping. It simple does not happen any more. Problem solved. Try it and you will see.
Rick