When you run your command at the shell, any unescaped wildcards are expanded according to what files they match. So if there are three files, 1.pl, 2.pl, and 3.pl in the directory, then this:

./rename *.pl "s/^/old_/"

# will be expanded to this:

./rename 1.pl 2.pl 3.pl s/^/old_/

# and set @ARGV like so:
$ARGV[0] == '1.pl';
$ARGV[1] == '2.pl';
$ARGV[2] == '3.pl';
$ARGV[3] == 's/^/old_/';
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So if you want to call it in that order, you have a couple of options. You can escape the asterisk in *.pl with a backslash or by putting it in single quotes, so that the shell will pass it to the script as a single argument, and it'll end up in $ARGV[0] as you expected. The other option is to allow the shell to expand the filenames, then get your regex from the last argument with pop, leaving the filenames in @ARGV:

my $pattern = pop @ARGV;
for my $file (@ARGV){
   my $new = $file;
   # apply pattern and rename
}
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If you use the second method, you don't need the opendir/readdir, because the shell is taking care of that for you. That method is probably simpler, but it's less cross-platform since it assumes the shell knows how to do wildcard expansion.