Possible damage to plywood decking by roofers?

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I have a 15 year old home with 5/8ths inch plywood decking over the trusses. After the roofers removed the original shingles and laid new tar paper and new shingles, I see a dip appearance between some trusses. There are also 3 foot long high spots at the trusses here and there. I think the roofers damaged the decking while installing the new shingles. Is this possible. The roof is steep but the workers could walk on it ok. The roofer claims these high spots were always there, I just didn't notice them before. Also, the hip shingles don't all lay down nice and flat. Anybody experienced this stuff too?