All above is correct. While you're better off, overall, changing the whole algorithm to using some File::Find variant, the simplest most direct solution to the problem, is to just replace the glob with an opendir, readdir combo. So, rather than:

$dir .= '*';
my @list = glob($dir);
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you could do:

opendir(DIR, $dir) or die $!;
my @list = readdir(DIR) or die $!;
closedir(DIR) or die $!;
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So that you're actually looking at the file contents, directly, rather than relying on globbing.