"what I did wrong"

The learned choroba answered that question; your program lacked recursion. I recommend using Path::Iterator::Rule for this kind of recursive file-finding exercise. I like its compact and clear syntax, as shown in this simple demo:

use strict; use warnings; use feature 'say';
use Path::Iterator::Rule;

my $dir = '1230046/public_html/software';
my $_numMissing = 0;
my $_filesThere = 0;


my $r = Path::Iterator::Rule->new->file->exists->and(sub {
    my $wanted = $_[0] =~ s!software/!!r;
    -e $wanted ? $_filesThere++ : $_numMissing++ && say "$wanted is mi
+ssing";
})->all($dir);


say "  Found: $_filesThere";
say "Missing: $_numMissing";

__END__
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Test directory structure:

ls -R 1230046

1230046:
public_html

1230046/public_html:
42.txt  43.txt  bar  quux  software

1230046/public_html/bar:
42.txt  baz

1230046/public_html/bar/baz:
42.txt  43.txt

1230046/public_html/quux:
43.txt

1230046/public_html/software:
42.txt  43.txt  bar  foo  quux

1230046/public_html/software/bar:
42.txt  43.txt  baz

1230046/public_html/software/bar/baz:
42.txt  43.txt

1230046/public_html/software/foo:
42.txt  43.txt  baz

1230046/public_html/software/foo/baz:
42.txt  43.txt

1230046/public_html/software/quux:
42.txt  43.txt
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Output:

$ perl 1230046.pl

1230046/public_html/foo/42.txt is missing
1230046/public_html/foo/43.txt is missing
1230046/public_html/quux/42.txt is missing
1230046/public_html/foo/baz/42.txt is missing
1230046/public_html/foo/baz/43.txt is missing
  Found: 6
Missing: 6
[download]

Hope this helps!