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This is curious. Hard for me to imagine the nut or bolt being close enough to interfere at that location, but we find all kinds of anomalies during our builds. If accessible, I'd see if rotating the fastener or placing the nut on the opposite side would help? Perhaps partial disassembly to access the fastener location will be needed. Builders oftentimes add inspection/access covers to the underside of wings for this sort of thing. After ruling out all other options, new rivet hole(s) next to this one may be fine. Good luck in resolving.
I used a steel screw to plug my hole, broke off, of course. Mark the other wing NOW to not drill out that hole, it will have same problem. There is another rivet with interference issues on each wing root. Both are discussed here on forum, somewhere. The one near the wing root hits a bolt or nut instead of the spar which you just hit. It is worth researching because you end up drilling and ruining a nut. I have it booked marked on my PC, but am on travel with only my tablet for the next week or two, so I cannot offer to look up a link. It has been a year since I had the same issues, still remember being a little vexed.
You can shorten the rivet:
Note that when doing this you are simply filling the hole, the modified rivet has lost its structural integrity and you need to drill two new holes on either side, equidistant to the other rivets and add new rivets to maintain the proper structural integrity. With my Cruzer I came across 2 or 3 locations where there was interference
Put the nut toward the front. Manually pull the rivet slowly. As the rivet becomes shorter push down into the hole.
if you push and pull the rivet slowly, because the rivet gets shorter as you pull it will seat properly when there was initially not enough room.