Visiting the USA from the UK on a passport with 3-months expiration

I last visited the US in August 2017 and flew into Fort Lauderdale from the UK. I applied for my ESTA in June which was granted, and travelled to the US on my passport (an e-passport) which expired in October 2017 (roughly, 3 months left on said passport at the time of travel). I was aware there was a requirement for passengers to be in possession of a passport with a minimum of 6-month expiry from certain countries for entry into the US, but when I looked online, the UK was exempt from this:

Are one-year passports issued by the U.K. government valid for travel?

Yes, the passport is valid for travel to the United States.

The fact that it may not be valid for at least six months beyond your date of departure from the United States will not affect your eligibility to travel.

The United States has an agreement with the United Kingdom automatically extending the validity of a passport for six months past the passport’s expiration date. Therefore, your passport need remain valid only for the duration of your stay in the United States.

If you are traveling visa free, and your passport is valid for less than 90 days, you will be admitted only until the date the passport expires.

(Source: https://uk.usembassy.gov/visas/non-immigrant-visa-faqs/passport-and-travel-documents/)

When I reached the automated security station where I was required to scan my passport, I received a message on the screen stating my passport did not have long enough left on it for the machine to process it. So I was ushered past the machine and into the immigration queue (the same queue which I would have joined if the machine had validated my passport).

I explained my situation to the immigration officer, and he said "We may have a problem here." I was tired and jet-lagged, and didn't fully grasp the situation, nor did I really question it. He went to speak to somebody in the back-room, came back, and permitted me entry into the US, but stated my ESTA is only valid until my passport expiration.

I don't understand what the problem could have been? And how having at least 6-months expiration on my passport would have cleared the problem. The ESTA lasts for two years, so surely the same situation could apply to somebody with 6-months expiration on their passport.