I removed the muffler to change the rear tire, put it back and never gave it another thought. UNTIL I opened the right side case and the rear hinge popped loose. I first thought it was broken until I removed the 'stay' and the front hinge also popped out. So now I see that the muffler interferes with the opening of the side case just enough to pop the hinge. I rearranged the muffler to give the maximum clearance but it still hits and if not careful, I think it would pop it again.

Anyone else experience this and if so, how did you fix the issue?

Oh sure, an aftermarket muffler......$$$$