Perl doesn't know that you intended to replace the running program with another process, thus the warning. The message says everything itself; you can try something like { exec($cmd) or die "exec: $!" } to supress the it properly.

<defunct> processes are zombies. Zombie is a kind of process which had finished running, but its parent has not handled SIGCHLD yet. This is strange; Parallel::ForkManager should handle these situations. To kill a zombie you simply need to kill its parent process (or wait for it to finish).