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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You need to determine the size of the smaller array and restrict the loop accordingly.

my $size = @data1 < @data2 ? @data1 : @data2;
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Thanks for the tips. It works.