That simply means that the value in one of the arrays is the null string ('') eg, a blank line.

You can either trun of that particular warning with

no warnings 'uninitialized';
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See perllexwarn for details.

Or you could modify the print statement to provide better diagnostics.

print OUT "line $_ differs. File 1: ",
    $file1[ $_ ] || '[blank]',
    " != File 2: ",
    $file2[ $_ ] || '[blank]',
    "\n"
    for $comp->full_compare(\@file1,\@file2);
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