PhD application recommendation letter from 2 supervisors who guided the same project? I need 3 recommendation letters for my US Science PhD application.

I have 2 supervisors prof. A and Dr. B who have guided my thesis project.

Prof A knows me very well. I have taken multiple courses and research projects under his supervision. He will no doubt give me an excellent recommendation.

Dr. B is a researcher at an institute. He knows me well and has co-supervised my thesis project. He might give me a good recommendation (possibly not as good as prof. A). He has a few personal contacts in some universities that I will be applying to. 

I have an inclination towards taking recommendation letter only from prof A. However, in specific universities, it might be helpful to have a recommendation from Dr. B as well, due to his contacts and reputation. 

Will it do more harm than good if 2 out of my 3 recommendation letters are from the supervisors guiding the same project (assuming that both the letters are positive)
You have to weigh asking B to write you a letter against an alternative.  If the alternative is somebody who does not know about your thesis work, they are probably will not know enough about you to write a letter that is as informative as the letter B would write.  

You can use a different strategy for each application.