The stability of a shear flow imposed along a diffusive interface that separates two miscible liquids (a heavier liquid lies underneath) is studied using direct numerical simulations. The phase-field approach is employed for description of a thermo-and hydrodynamic evolution of a heterogeneous binary mixture. The approach takes into account the dynamic interfacial stresses at a miscible interface and uses the extended Fick's law for setting the diffusion transport (the diffusion flux is proportional to the gradient of chemical potential). The shear flow is unstable to two kinds of instabilities: (i) the Kelvin-Helmholtz instability, with an immovable vortex formed in the middle of an interface (in the vertical direction), and (ii) the Holmboe instability, with travelling waves along the interfacial boundary. The development of the Holmboe instability results in a stronger enhancement of molecular mixing between the mixture components. Earlier, the boundaries of these instabilities were determined using the linear stability analysis and employing the concept of a 'frozen interface'. In the current work, through the solution of full equations, we obtain the stability boundaries for several sets of governing parameters, showing a greater variety of the possible shapes of the stability diagrams. The Kelvin-Helmholtz instability always occurs at lower gravity effects (lower density contrasts), while the Holmboe instability occurs when gravity is stronger. We show that for some parameters these two instabilities are separated by a zone where the shear flow is stable, and this zone disappears for the other sets of parameters.