Twisted bilayer graphene (TBG) hosts a set of moiré bands which become flat in the magic angle limit. As part of my PhD I investigated how lattice defects such as non-magnetic impurities and vacancies in TBG induce charge modulations both in the atomic and moiré scale due to the presence of these moiré bands. At the same time, an important open question in the field is the pairing symmetry of the superconducting state of TBG, which is enabled by the flat bands. The extreme sensitivity of the flat bands with respect to defects points to a probable strong interplay between superconductivity and atomic defects in TBG. In this project I will explore how this interplay takes place, with a focus on differentiating the response of different pairing symmetries. An understanding of this process would represent a significant contribution to the understanding not only of TBG but of moir\'e systems in general.