I'm looking for some advice on what to do with a roof job gone bad. We hired a roofing and siding company to come and replace our roof and install new siding. To keep the story short, they came and installed the roof which it appeared to be a good job. Then the siding crew came to do our raised ranch. When it came to do the upper section they put up scaffolding. Here's where the problem starts. They didn't lift the shingles and put the screws through the shingle underneath. THEY WENT RIGHT THROUGH THE TOP. WHEN THEY WERE DONE THEY FILLED THE HOLES WITH CLEAR SILICON. When we were on the roof we noticed these little silicon dots and saw the pattern. Well we complained that now they have no only ruined the rubber ice sheet under but have about 30 holes in our new shingles. They said they would replace the shingles but is this the right solution? These holes are in the first 2 courses of shingles on both the front and back of the house. What should they do and what should I watch for?