I thought they put tarps down when they were removing the old roof to avoid this? You got swindled!
Yep, I've had a few roofs done and they always get all the nails. Usually you don't pay the last 1/3 til the whole job is done and that's when you should be checking for nails. And the tarps are for not only only the nails but the shingles too, quicker clean up.