It is unfortunately not uncommon, for a roofing job to end in dispute when you’re dealing with less than reputable roofing contractors. This problem arises out of simple issues, like water damage.
The reason this is common with less than reputable roofing companies, is because they usually fail to set proper expectations, and usually lack the proper documentation and contracts.
Before signing a contract, be sure that it contains language addressing who is responsible for any damage that occurs as a result of the roofing work.
This would make it clear who is responsible, but it would also make it clear whether or not the roofing contractor is a responsible contractor in general.