The structure of your roof below the area that was replaced may be the problem causing your leak and not the new roofing material itself. If the roof’s initial design is weak it can potentially cause the roof membrane to split under heavy loads, such as hard rains, and allow water to leak through to your ceiling. Unfortunately the roof supports would have to be rebuilt to prevent this from happening.
The slope and any sagging of the roof structure can cause pooling of water on the roof and cause leaks through the roof membrane. This is also a structural issue that may not be the fault of your roofer. If you have inadequate drains for the roof causing ponding of water you may be able to have modifications done to the roof to stop the problems from happening.
Some roofing materials can contract and expand as temperatures change. This is especially true of metal roofs. If the roofer did not allow for some expansion and contraction of the roofing material, the changes in temperature could cause the fasteners or nails to wallow out the holes where they are attached to the roof. This could allow water in through the fastener holes, which can lead to leaking from your ceiling. If you suspect this problem, you should contact your roofer about it.
One of the most common places for roofing to leak, whether old or new, is at the flashing. Flashing is installed as a barrier between the roofing material and other parts of the structure such as chimneys protruding from the roof or edges between roofing sections. If the roofer did not install proper flashing or didn’t install it correctly then water can leak into these areas and cause a ceiling leak below. If you suspect the flashing is the source of your leak you should have the roofer come out and have a second look at his work.
If you installed a new roof on top of old roofing material instead of having it removed, you could be setting yourself up for problems. If you have more than two layers of roofing material on your home it might save you money as opposed to removing the old roof first, but the weight of the materials as well as potential rotting problems underneath could make your new roof unstable and prone to leaks.