When you say that they put new plywood over the old, what was the old? Was it old plywood? The next questions is why did they put wood over wood? Did they build it up to create an air gap or did they lay it right over the top?
Normally the only time we install wood over wood is in 100 year old houses with spaced decking and we need a nailable surface. This isn't a problem is you fix the bad wood first and nail into the existing rafters. That's the key nailing into the rafters.
It could also be that they didn't use the proper nails. I have seen roofers use roofing nails to nail wood, which require a different kind of nail.
It sounds to me like possibly the problem may be that they didn't nail into the rafter, that possibly they nailed the new plywood into the old wood. You won't get enough holding power doing this. If this is what they did, the roof needs to be replaced.
it could also be possible that perhaps they did not leave a 1/8" gap on all sides of the plywood for expansion and contraction. We like to place a nail between the boards to get this proper gap. If wood is cold and contracted when it is January and now it's the hot steamy summer and wood is expanded, it needs a place to go, thus the gap. If no gap you get a wavy roof surface with wood buckling at the plywood joints. If this is what they did, your roof needs to be replaced.
I'm really curious why they put wood over wood and didn't tear off the old wood. But it could have nothing to dow ith the wood. Cold weather roofing is very picular requiring numerous additional attentions to details you need to worry about, that you don't need to worry about the rest of the year. This is why I am not an advocate of winter time roofing. It could be the same expansion and contractors issues mentioned above, but expansion of the shingles instead of expansion of the wood.
Is there any way you can post a picture?