Your inner loop:

 foreach $ip(@ip) {
   print $out "#" if(/\b$ip\b/i && !/^#/); #only one # at front of lin
+e
   print $out $_;
 }
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Calls "print $out" once for each item in @ip, causing double lines. The simplest fix (untested) is early exit:

 foreach $ip(@ip) {
   last if /^#/; # ALready has a hash . Note - LAST exists this loop
   next unless  /\b$ip\b/i; # No match - so try the next item
   print $out "#";
   last; # Remember to exit loop after one successful match
 }
print $_; # Print onloy once.
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When you are ready, take the next step and learn regex alternation, for a more efficient solution.