Si dangling bonds without H termination at the interface of quasi-free standing monolayer graphene (QFMLG) are known scattering centers that can severely affect carrier mobility. In this report, we study the atomic and electronic structure of Si dangling bonds in QFMLG using low-temperature scanning tunneling microscopy/spectroscopy (STM/STS), atomic force microscopy (AFM), and density functional theory (DFT) calculations. Two types of defects with different contrast were observed on a flat terrace by STM and AFM. Their STM contrast varies with bias voltage. In STS, they showed characteristic peaks at different energies, 1.1 and 1.4 eV. Comparison with DFT calculations indicates that they correspond to clusters of 3 and 4 Si dangling bonds, respectively. The relevance of these results for the optimization of graphene synthesis is discussed.