In glancing through the code, if appears that something in or around the line in sub _get_reports()

$problem .= "$site_folder ";
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would have to be involved. Expanding the search out from that point I see that the array  @site_array is being looped over and that $problem is being reset just before it. Hmmm, that seems Ok.

Branching out to the next loop I see that @site_array is initialized before the outer loop (which walks thru the reports) and not always within the loop.

I think that is the problem. The @site_array array is initialized differently depending on  $site_locations. In the 'All' case new sites are pushed onto the array leading to an accumulation of the sites and the problem you are seeing. So, I think you need to clear the array in that case.

  if ($site_locations eq 'All') {
      @site_array = ();  #clear the array
      for my $site (sort keys %$sites) {
               push @site_array, $site;
      }
   ...
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I have not tested this, it's just my first guess. I hope it helps.

FWIW: My litte Rant; I used to produce "Write-Only" code until I had to debug some crap I "Wrote" in the past and did not have the faintest clue what I had done or why. I comment code now! :-))