We study the atomic scale microstructure of non-stoichiometric two-dimensional(2D) transition metal dichalcogenide MoSe2-x, by employing aberration-corrected high-resolution transmission electron microscopy. We show that a Se-deficit in single layers of MoSe2 grown by molecular beam epitaxy gives rise to a dense network of mirror-twin-boundaries (MTBs) decorating the 2D-grains. With the use of density functional theory calculations, we further demonstrate that MTBs are thermodynamically stable structures in Se-deficient sheets. These line defects host spatially localized states with energies close to the valence band minimum, thus giving rise to enhanced conductance along straight MTBs. However, electronic transport calculations show that-the transmission of hole charge carriers across MTBs is strongly suppressed due to band bending effects. We further observe formation of MTBs during in situ removal of Se atoms by the electron beam of the microscope, thus confirming that MTBs appear due-to Se-deficit, and not coalescence of individual grains during growth. At a very high local Se-deficit, the 2D sheet becomes unstable and transforms to a nanowire. Our results on Se-deficient MoSe2 suggest routes toward engineering the properties of 2D transition Metal dichalcogenides by deviations from the stoichiometric composition.