The ?? at the end of your regex looks a little suspicious. One question mark would mean "match the string <?query?> zero or one times". Do you really want the 2nd question mark un-escaped there?

It would have been more helpful if you had provided an example of the $data_in string. Is this what you had in mind? ...

use strict;
use warnings;

my $data_in = '<container><a>bbb</a><b>cccc</b></container><?query?>';
my $data_out;
while ($data_in =~ /<container><a>(.+?)<\/a><b>(.+?)<\/b><\/container>
+(<\?query\?>)?/ig)  {
    print "1=$1\n";
    print "2=$2\n";
    print "3=$3\n";
    $data_out = "$2, $1$3 ";
}

__END__
1=bbb
2=cccc
3=<?query?>
[download]

Of course there is probably a much simpler way of achieving this.

I agree with Fletch that you probably would be better off using a CPAN parser than your own regex solution.

Update: Another general note on regexes. You can use alternate delimiters in order to avoid excessive escaping of forward slashes. For example, you can replace // with m{}:

while ($data_in =~ m{<container><a>(.+?)</a><b>(.+?)</b></container>(<
+\?query\?>)?}ig)  {
[download]