Hi Jon,
I am an experienced roofer, but please bare-in mind, I am not a professional. I can tell you from experience that it is possible for a "brand-new" shingle to be broken under sustained winds, especially in the cooler months. The reason this happens is because the adhesive tar-strip on the underside of the shingle is heat activated. Eventually the sun's heat bonds the overlapping rows of shingles and causes the entire roof to basically become one layer. During winter, and cooler months it takes a little longer for the tar strips to bond.
Another area of the roof that is prone to loosing shingles is the ridge cap. The ridge cap is not as secure as the shingles on the flat areas of the roof. The individual shingle caps usually only support four nails, rather than the six or seven along the run.
If your neighbors had some leaks, chances are, water came through the ridge because a cap or two had been blown off. However, this is your home and your investment. If it were me, I would climb up on the roof and watch how many nails they're fastening each shingle with. I've watched pro's shoot so fast they leave up to 12" of shingle without a single nail.
Some other problems occur when roofers are in a hurry to finish, either because of money, weather, or just poor oversight and training. Some guys put nails right into the edge of a shingle. This is something the manufacturer warns against because nailing too close to the edge can result in a leak, nails should be (at least 1") from edges. There is also a certain area of the shingle where two layers overlap and add strength where it accepts a nail, but too often nails are shot above or below this area because the roofer does not know about it, or they are trying to be a "super-roofer!" Another mistake, but a very rare mistake I have noticed is using nails that are too short. But the number one mistake is not laying the felt correctly, or even worse, felt missing in some places or no felt at all!!!
Good luck, and remember, don't be afraid to approach your contractor with any questions.
-Chris in FL