We have investigated the role of heterogeneities in the intrinsic topological superconductor FeTe_0.55Se_0.45 single crystal, using scanning tunneling microscopy. High spatial and spectral resolutions at ultra-low temperature (40 mK) and under high magnetic field (9-2-2 T) allow us to study putative Majorana bound states (MBS) at the vortex core. Isolated MBS are revealed at vortex core and distinguished from complex in-gap states near zero bias. The relatively large superconducting gap of FeTe_0.55Se_0.45 enables us to evaluate how Caroli-de Gennes-Matricon states suppress superconductivity at the surface steps, and how subsurface defects give rise to in-gap states in high magnetic field. The understanding of heterogeneities in intrinsic topological superconductors will facilitate the realization and control of MBS for creating error-tolerant qubits.