It's good that the roof is not leaking (you didn't mention that) but improper installation will create leaks in the future. So, verifying a few key items and then officially notifying your builder (by certified, return receipt mail) of incorrect installation will protect your rights. I'd check the following:
Number of nails in each shingle: Each roofing manufacturer requires a certain number of nails into each shingle, usually 4 minimum. Depending on your location, it could be 5 or 6, depending if you are located in a "high wind area". (Where I live, 65 mph winds would require 5 nails per shingle.) You'll find this info on each wrapper around each bundle of shingles. If no wrapper is around, you can find it on the manufacturer's website. If you don't know the name of the manufacturer, call the builder.
Nail Placement: I see this wrong on a lot of jobs. If nails are placed too high, then the nail will not penetrate the top of the shingle on the layer directly below. Nails should be above the top of the cut out in the 3-tab shingle, but about 1" below the mastic strip. Most roofers want to nail "in" the mastic strip. This is bad for two reasons: a) it misses the shingle directly below, so there are only 4 nails holding the shingle on the roof instead of 8 nails, and b) it creates a little dip in the shingle because it causes the shingle to bend down over the top edge of the lower shingle.
Lack of Hand-Tabbing: Most shingles do NOT require hand tabbing, unless you are in a "high wind area". Hand tabbing is placing a quarter size dab of roofing mastic "by hand" under each shingle. However, most roofing manufacturers require hand tabbing "if the shingles have not self-sealed in a sufficient time." This is a bit arbitrary, but "sufficient time" means "within the guarantee period." (You can get that confirmed by the roofing manufacturer.) So, the way to test this is to go up on the roof and try to lift a shingle tab (bend a shingle tab up). I'd try about a third of the shingle tabs. The roofer will tell you the shingles will "self tab" down. That means they anticipate the sun heating the shingle up until it sticks to the mastic strip under each tab. The problem is that it may not get warm enough in your area or the nails are not set flush and the nails are holding the shingles up above the mastic strip. (See #7, below.)
Too large of exposure: Three tab shingles should have only a 5 5/8" exposure. Most roofers will stretch that to 6" or 6. 1/2". That gives the opportunity for the wind to lift more of the shingle and creates improper nailing, (missing the top of the lower shingle, etc.)
Too short of nails: Nails should completely penetrate the plywood. Can you see the nails from inside the attic?
Roof sheathing is too thin: 1/2" plywood or 5/8" particle board minimum, I think. Check with manufacturer. Again, this info is on the wrapper.
Nails or staples are not set flush: That is to say the nails are held up slightly (maybe 1/8") which keeps the shingle from self-sealing.
These are the things that lead to blow off, but other typical bad roofing issues are: A) no starter course, B) shingle ends are not staggered, C) blown off shingles not repaired correctly and the holes in the paper underlayment not sealed correctly where nails have withdrawn from blow off.
One thing that seems odd is that various shingles are blowing off. Usually, one shingle blows off and it takes 10-12 more shingles above it in a "V" shape pattern. This indicates to me, that the nails are not in the correct position below the mastic strip, (see item #2, above.)
Also, where I live, by law, roofing has to be guaranteed for 2 years not 1 year. So, your guarantee period may go another year. You can verify that with your state's Construction Contractors Board (CCB). Also, check the roofing manufacturer's wrapper.
