It does not actually run the transaction through the entire way - if a transaction fails, the card info gets placed on a blacklist and that particular NFC device won't receive an instant authorisation next time. Generally speaking, people don't have an easy way to generate lots and lots of fake NFC devices, so this hasn't been a problem for widespread fraud (vs just jumping over the turnstile).
The killer feature that also causes most of the quirks is that it can be used to make payments fully offline without allowing double-spending of balance. This is of course mostly a killer feature for transit operators rather than users. OMNY solves the same problem by just accepting that it'll occasionally permit free rides.
I remember when the clipper cards rolled out. If I saw more than a few people holding one, I’d just go to the other gate.
These days, I can't remember the last time I had an issue with my physical Clipper card. I do recall lots of issues when they first rolled out the ability to put a Clipper card on your phone, but I haven't run into a problem with that in at least a couple years.
I forgot to get a Tokyo metro pass along with my train ticket from Narita to Tokyo, so I ended up wandering around Nippori station looking for an ATM that would take my Visa debit card so I could get some cash in order to top up my Pasmo card[0] and take a local train to Shinjuku. I'd also forgotten how most random ATMs don't take foreign debit cards; after it dawned on me, I left the station, found a 7-11, and used the ATM there.
This was not something I enjoyed having to do, while carrying my bags, after a 10-hour flight, plus 2 hours waiting in line at immigration, followed by another hour-long train ride to the city.
I was pleasantly surprised to find that many many more businesses in Japan take credit cards nowadays though.
[0] I was also pleasantly surprised to find that Pasmo cards are still good up to 10 years after the last time you use them. I feel like something similar in the US would expire after no more than a year or two.