It is documented behavior.

"Care should be taken with the values that are substituted. The formula returned by repeat_formula() contains several other tokens in addition to those in the formula and these might also match the pattern that you are trying to replace."

Try this instead:

#!/usr/local/bin/perl -w
use strict;
use Spreadsheet::WriteExcel;

my $workbook = Spreadsheet::WriteExcel->new("test.xls");
my $worksheet = $workbook->addworksheet("foo");

my $formula = $worksheet->store_formula('=SUBTOTAL(9,A1:B1)');

foreach my $row (0..99) {
  $worksheet->write($row,0,$row+1);
  $worksheet->write($row,1,$row+1);
  $worksheet->repeat_formula($row,2,$formula,undef,qr/A1\b/,'A'.($row+
+1),qr/B1\b/,'A'.($row+2));
  $worksheet->repeat_formula($row,3,$formula,undef,qr/A1\b/,'B'.($row+
+1),qr/B1\b/,'B'.($row+2));
}
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