The most likely scenario was that this merchant reports transactions in batch, something broke on their end and it either took them a long time to realize it and/or fix it and/or catch up on the orders.
The party that you're putting your trust into is the merchant as much as, if not more than, CJ. It is in the merchant's power to screw up the reporting of transactions.
CJ and any other network does everything they can to ensure that 100% of transactions are reported. They get paid the same way you do, on performance.
This is not an uncommon occurance. Transaction reporting gets delayed, recovered, and usually all fixed up. It's annoying, even harmful, especially if you're buying traffic, but ok stuff happens.
To me, what's unacceptable is that merchants and networks tend to not talk about these things when they happen and clean up quietly with hopes that nobody notices. They want to wait until they know the good news before delivering any bad news. It can take days and of course everybody notices.
I've never, ever, seen a proactive communication that something went awry go poorly. I've seen dozens of non-communications blow into something much bigger than necessary.