Nothing new there
@Rice (I don't mean just you being the victim all the time
)....
The authorities don't like repetitive exempt entries - never have, and they have periodic purges. I believe that it comes under their umbrella of 'having the appropriate visa to match your circumstances in Thailand '....visa exempt is for short-term tourism; being married to a Thai (or having retirement accommodation) does not fit with visa exempt.
Classic case is workers in the oil and gas industry who typically work one month on, one month off. Visa exempt suits them perfectly - but it doesn't suit Thai Immigration who would rightly claim that the visa exempt system was being abused when they were effectively living in Thailand for half the year.
IMO the situation you described (not sure if 1 x 3 month Non-O and 1 x visa exempt is the full story) you were not abusing the system - the Non-O was appropriate for what was a longer stay and no one in their right mind would pay for another visa if they knew they were staying less than a month.