Executing your script with the provided files yields the following results for me:

> perl script.pl file1 file2
cd, 2343
ef, 1253
ij, 2343
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Is this not the expected result? I suspect your issue is on your command line.

On a side note, it is very dangerous to pass a command line argument directly to a two-argument open as you have done - it allows execution of arbitrary code. You should also check out using the pragmas strict and warnings to save you some potential headaches. Might I suggest the following code?

#!/usr/bin/perl
#
#
use strict;
use warnings;

my $file1 = shift;
my $file2 = shift;
my $match = 0;

open(IN, "<", $file2) or die "Cannot open file $file2 $!\n";

while(<IN>){
   chomp($_);
   my $s_line = $_;

   open(INPUT, "<", $file1) or die "Cannot open file $file1 $!\n";

   while(<INPUT>){
        chomp($_);
        my $str = $_;
        if($s_line =~ /$str/){
        $match = 1;
      }
   }
   close(INPUT);
   if($match == 0){
   print "$s_line\n";
   
   }
   $match = 0;
}

close(IN);
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