I would guess its a foreign object still left in the tire. Usually the most obvious reason is the correct reason

I must be very lucky. I have close to 4000 miles on my 2010 Roubaix (stock wheels with replaced cheapo tires) and can honestly count on one hand the number of flats I have had. I started riding the Roubaix at 320 lbs (now down to 280lbs) but ride VERY defensively. I avoid potholes, ridges and ride out of the saddle over rough road. I even rode 204 miles over 2 days and not a single flat. Tubes I have replaced are from any cheap source, even Walmart. I ALWAYS pre-check my tire pressure on any ride over 5 miles.