Clearly CO screwed up and probably owes you some compensation (good luck).
But I do have to say that this would have been avoided if you had been more educated -- specifically knowing to check that you have an e-ticket number for all your reservations. And now you know that, so consider yourself educated.
One missing piece -- shouldn't PayPal have emailed you when the payment "expired" after 30 days? Was this trip planned more than 30 days in advance? If so, did they e-mail you? I would take that issue up with PayPal.