When a contractor starts to do any work, the first thing they should do is to look at what they are working with and give a price based on what they see and what they think it will cost to do their work based on what they are working with.
In the case of remodeling/repairs/alterations/re-roofing there may wall be things which are not visible when the estimate is given. That means when the contractor (roofer in this case) removes the existing roof they can now see what was hidden from them when they looked at it before giving the estimate.
At that time, with the old roof removed and the substrate exposed (roof decking), they now have full view of what they are working with, and it is their responsibility to either accept or reject what they find to work with BEFORE starting to work installing the new roof covering.
With the old roofing removed and the roof decking exposed, the roofer had the opportunity to assess the roof BEFORE starting to install the new roofing, and if they did not like what they saw, it was their obligation to let the association know that something was wrong with: the decking (rotted, installed wrong, wrong type, etc.,); the design (valleys dead-ending into walls, chimneys in the center of valleys, etc.). It would then be up to the association to agree to have what is wrong corrected (by that contractor or by another contractor) or to accept what was wrong and having been advised that not correcting what was wrong will not allow a "proper" re-roofing to be done, and that not correcting what was wrong may lead to leaks.
If the contractor finds nothing wrong, they proceed doing the work (installing the new roof covering), or, if the contractor finds something wrong but decides that 'I can work with it' and 'it will be okay to proceed starting work', then the contractor BOUGHT THE PROBLEM by accepting what their work was going on.
Unless that roofer brought the "design flaw in the roof" to the attention of the association and the association accepted the design flaw and told the roofer to 'work with it as best you can' ... if that did not happen and the roofer accepted the roof design and installed the new roof, then the roofer has no one to blame except himself as they 'accepted' the 'design flaw' when they installed the new roof covering.
At this point, I recommend telling the contractor 'No problem, go ahead and correct the design flaw ... AT YOUR COST ... because you accepted the roof design when you installed your work on that roof design and did not advise the association that there was a design flaw with the roof when the roof was exposed.' Then add 'It is not our responsibility to pay for your work twice when you were the licensed contractor who accepted the roof design as it was.'
No knowledgeable contractor will start doing their work on an unacceptable surface unless directly directed to do so, backed up with paperwork showing that the contractor reported the unacceptable work surface to the owner and was told to do the work anyway.
If contractor told the the association about the design flaw when the roof was replaced, and the association told the contractor to do the work anyway - then the association needs to be the one to bite the bullet and pay whatever it takes to make the design work properly. I doubt this happened, but it does happen on occasion.
More frequently, it is the contractor who does not inform the owner of the unacceptable surface and proceeds to do their work anyway, then they expect the owner to pay again when their work fails because the surface was unacceptable. The problem with this scenario is that the contractor "accepts" the surface once they start working on it and do not disclose it to the owner, at that time, the 'unacceptable surface' now becomes an "acceptable surface" because the contractor "accepted" it.
Yes, there are roofing experts and roofing consultants. there are also some very well qualified independent inspectors who can serve as 'experts' in various categories, including roofing. Where in Colorado are you located.
Jerry Peck - CodeMan
Construction and Litigation Consultant
Construction Litigation Consultants, LLC.