The paper describes a numerical method that considers specific computational fluid dynamics (CFD) aspects of viscous incompressible flow simulations in the vicinity of interfaces between unmatched fragments of unstructured grids. The method is based on the general grid interface (GGI) principle, which involves conservative flux interpolation and does not require original grid modification at unmatched interfaces. A method is presented which combines adjacent unmatched fragments of an unstructured grid into a single domain by means of virtual interfaces considering connections between adjacent cells through virtual faces. The performance of the method is illustrated by the finite-volume discretization of the transport equation in the region of matched interfaces and its modification for the case of unmatched interfaces. The efficiency of the proposed method is demonstrated by three-dimensional CFD simulations with grid models composed of unmatched unstructured grid fragments. The simulation results are compared with equivalent simulations on matched grids. The influence of unmatched interfaces on the convergence rate and accuracy of the solution is assessed.