Should a roofer put a nail through the outside of a shingle?

I had a new roof installed over a month ago. There were a lot of shingles that never flattened out. I live in Houston so yes the temperature got hot enough. I complained to the roofing company, so they sent a couple of guys out who hammered nails through the outside of the shingles and smeared a little roofing cement over the tops. Will this void the warranty of the shingles, and are they at risk of leaking?