Who is responsible for the follow up repair, the original contractor or their subcontractor?

First of all, the $900 is an exuberant amount to pay for one room of ceiling work. Should only be half that and that would be high end.(unless you have vaulted or very high ceilings) Considering that the materials would be less than $200. As for who is responsible, it is whomever you signed a contract with. If you did not sign the contract with the subcontractor which I do not see why you would then it would fall to the contractor. Of course if you did not report the problem until now, and there is no warranty on the craftsmanship of the ceiling then you are simply S.O.L. and will be stuck with the repair bill. Most work when completed has no warranty unless otherwise issued in writing and complaints have to be lodged almost immediately. My recommendation is to look through the warranty of the roofing contractor and if it is not warrantying anything from it's subcontractors you should just find someone to do the work right for the lowest cost you can. Make sure the work is done right before you pay them ANYTHING. If someone asks for money upfront for materials or any other reason they are not reputable. And make sure you have a contract in writing so they can not over charge you after the work is done and force you to pay more or have a lien put against your property.