Previous block of code (while (..) {..}) used to wait threads to finish (I think).

No, it waits for the queue to be empty, which isn't quite the same thing.

I'm pushing undef into the queue with

foreach ( 1 .. $config->{number_of_threads} ) {

    $q->enqueue(undef);
}
[download]

and I think this will cause thread to return:

    while ( my $org = $q->dequeue() ) {

        parse_org( $org, $mech );
        $pq->enqueue($org);
    }

    say "Finishing worker [$thread_id]";

    return;
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Also I have Finishing worker [SOME_ID] in the output...

I'm pushing undef into the queue with ... and I think this will cause thread to return:

It will. Eventually. But there is no guarantee -- indeed it is most unlikely -- that all of the threads will: a) get a timeslice; b) receive the undef from the queue; c) act upon it and exit; before your main thread tries to join them.

The whole point of join is that it waits for the threads to finish, thus ensuring that your main thread doesn't exit before your child threads are finished.

It rarely makes any sense to turn it into a non-blocking operation by calling is_joinable before calling join.

The are a few specialist uses for that, but in the case of your code it only guarantees that any thread that is slow to finish will not get joined before you terminate the main thread; hence the error message.

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Here you go ... just because queue is empty, doesn't mean threads are joinable
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This reliably exits with 6 running and unjoined on my old machine, YMMV

If you can make the code run .. and reproduce the problem, you can see the only real way to wait is to join everything not merely the immediately joinable :)

Previous block of code (while (..) {..}) used to wait threads to finish (I think). But may be I'm wrong :-(

Maybe, it depends on more code than shown I think :)

safest way to wait for threads to finish is to actually wait for them to finish :) blockingly  $_->join for threads->list