array @port_list which I get by reading a input file

Maybe your error is in the reading code which you haven't shown.
Have you Dumped @port_list to check ?

Update ; It looks like you may have leading spaces on the duplicates. Try adding another regex line

foreach my $val (@port_list) {
  $val=~s/\s+$//;
  $val=~s/^\s+//;  # add
  print "[$val]\n";
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poj