(I honestly have no idea, I'm not involved in manufacturing.)
As a tester, you build a 10k ($10M) unit test run and none of them fail, and then another 10k ($10M) run and again none of them fail... statistically you might not expect reliably catch a single failure until you run 10 times.... that's a $100M test you need to get your boss to sign off on.
Note that when you get a failure it will burn up and you won't be able to identify the cause.
Now, if you knew the failure mode, you could test for it directly and you wouldn't have to waste an entire assembled phone in a destructive evaluation, but that's hind sight. The failure defects they see seem like pretty standard problems, but other than sampling, I'm still not sure how they are going to catch them in manufacturing.
What's amazing is that more batteries don't go up (the original Prius was notorious).
Catching problems like this can be pretty tricky and at the end of the day it's also possible that a few people getting lazy and programming the machines wrong led to this.
There were 2 battery suppliers, the initial recall was done because batteries from the first supplier (a Samsung subsidiary) had structural/design defects.
To make up for this lost capacity, they ramped up production at the second supplier without much of a heads-up. Unfortunately the Quality Control was not adequate for the higher volumes, resulting in well-designed but sloppily made batteries that were also prone to explode. The problem in the second case was not a structural one, but in the manufacturing process.