For what it's worth, I can't replicate it with a different type of tied array.

use strict;
use warnings;

use Tie::File  qw( );
use Tie::Array qw( );

for my $module ('Tie::File', 'Tie::StdArray') {
   print("$module:\n");

   tie my @array, $module, 'tiefile';
   push @array, "[$_]" for 0..2;

   print(scalar(@array), "\n");
   @array = sort @array;
   print(scalar(@array), "\n");

   print("\n");
}
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Tie::File:
3
4

Tie::StdArray:
3
3
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