But it's still unclear which logic you expect, because thats a perfect set operation.

Could it be that you want to compare arrays one by one by position?

Then please use a loop to do so.

Yes, I would like to compare the arrays one by one by position. I have attempted following:

use strict;
use warnings;

open (FILE, "a") or die "Unable to open ref file.\n";
my @data1 =<FILE> ;
close(FILE);

open (FILE, "b") or die "Unable to open new file.\n";
my @data2 =<FILE> ;
close(FILE);
my $i;

for( $i = 0; $i < 2; $i++){
       if ($data1[$i] ne $data2[$i]){
        print "Mismatch for $data1[$i] and $data2[$i]\n";
        exit;
    }
}
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But the error occurs when file 1 contains one line and file 2 contains 2 lines.