If they've replaced the gfci breaker, it's not the breaker.
A dipole gfci breaker is a PITA. If there's no neutral, as some one said earlier, it compares both hot leads. The only thing that was wrong in the explanation is that it compares current, not voltage. If there is a 6 mAmp difference, it'll trip. Now, several things could cause it. One, the pump has a nick somewhere inside that causes an intermittant difference between hots. Two, the ozonator has the same issue. Three, once in awhile one hot leg runs a slight bit different than the other leg and the gfci senses an imbalance and trips. In other words, a pita nuicense trip.
They could put the ozonator on the blower breaker and only have the pump on the gfci. That would rule out the ozonator as an issue. At this point, changing the pump out would be the only thing else to try. The once a week or so incidence would lead me to think there's an intermittent difference in the hots, but that's only a guess. Gfci breakers with a neutral aren't as prone to nuicense trips.
FWIW, I agree with the pool builder. It's a stupid rule. A gfci outlet was always required for a pump that plugs in. Makes sense because someone could unplug or plug it in and it is outside. Now, for a direct wired pump, no one is plugging in or unplugging anything. Up until 2008, a hardwired pump didn't require a GFCI breaker. Matter of fact, there was quite a bit of debate about putting it in. Mine was put in under the 2005 NEC and has a regular 240, 20 amp breaker. If I thought it was an issue, I'd put in the gfci. However, it doesn't worry me in the least not having one.