Man, I feel this one in my bones. Had almost the exact same thing happen on a deck rail job about six years back, guy with 30 years telling me primer was a waste of money on cedar. Peeled so bad by the next spring that whole sections came off in strips you could read a newspaper through. Here is what saved me on the redo, scrape everything down to bare wood, sand the edges so you do not see the old paint lines under the new coat, then spot prime every inch of bare wood with a real oil or shellac based primer. The combo stuff just does not bite into raw wood grain the way a standalone primer does, it sits on top instead of soaking in. And do not trust the weather window either, Tacoma moisture will find every spot you rushed.

How'd you finally catch it was off?

The merge glitch was the real culprit here, not your work. Clients saying sorry is just their polite way of starting a call, not proof you messed up. Fixing it in a day with a manual check shows you handle problems fast, which most people appreciate more than a perfect system.