Thanks for reporting this @achasik. @mlandauer is away so, for my sins, I'm now looking after morph.io until he returns in October.
I've now restarted the queue, as Matthew advised we should do when this happens, and it's working again. He told me that this issue was still happening every few days so I've been trying to keep an eye out for it but please post in here if you see it happen again.
Thanks again for looking out for this!