If you drive through a deep puddle you should expect the brakes to be less effective. Wet brakes don't work as well as dry ones. Sometimes dramatically so. If you are also noticing it when wetness is not a factor, then you may be having a problem with the power brake booster.
Intermittent problems can be very hard to diagnose correctly. If you can, keep track of exactly when and under what circumstances the problem arises. It may help the technician come to a proper diagnosis. Unless you're still under warranty, it may work out better for you to go to a reputable local shop rather than driving an hour to the dealer. Ask around for recommendations.