You print once for every pass of the inner loop (4*2 times), but you only want to print once for every pass of the outer loop (4 times). Fix:

foreach my $adv79key (keys %adv79) {
   my $old;
   foreach my $exerrors (@exerrors) { 
      if ($adv79key == $exerrors) {
         $old = 1;
         last;  # shortcut.
      }
   }

   if ($old) {
      print "$adv79key is an old error\n";
   } else { 
      print "$adv79key is a new error\n";
   }
}
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Simplified (but removes shortcut):

foreach my $adv79key (keys %adv79) {
   if ( grep { $adv79key == $_ } @exerrors ) {
      print "$adv79key is an old error\n";
   } else { 
      print "$adv79key is a new error\n";
   }
}
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Optimized for speed:

my %exerrors = map { 0+$_ => 1 } @exerrors;

foreach my $adv79key (keys %adv79) {
   if ( $exerrors{0+$adv79key} ) {
      print "$adv79key is an old error\n";
   } else { 
      print "$adv79key is a new error\n";
   }
}
[download]

The "0+"s are probably optional. Just trying to be as close to the original as possible.