The easiest way to handle this would be to log off before the box shuts down, so it doesn't hang the ssh session. You could try replacing the shutdown command with this (untested):
(sleep 3; shutdown) & exit
You will want to change the sleep 2; call in your script to be considerably longer to give the remote system a chance to shut down, reboot and start up its ssh daemon. Or, better, enclose the last call to Net::SSH::Expect->new in a loop and retry it a reasonable number of times, sleeping a while between tries. This will let you connect reasonably quickly without dying if the remote system unexpected takes longer than usual to reboot (for example, if you are running SELinux and the /.autorelabel file exists.)
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