We will need a picture to show us just what the situation is. Most guns will mark the cylinder where the bolt comes up and hits the cylinder. That is normal. You might also have some preening in the notch itself if you have 'fanned' the gun. Fanning puts extreme stresses on the gun as the bolt comes up and suddenly stops the cylinder as you are still slamming your hand down on the hammer. Please get us a picture so we can correctly diagnois the problem. If there was an alignment problem, it would be spitting lead and you would know it.
PS. Have no fear of Taurus' warranty service. I just received a Gaucho back for an incorrectly cut half cock notch on the hammer and I am very pleased. Service took 4 weeks, including the shipping but they took care of the problem for me. 44 Man