Modeling pore-scale processes is important for understanding the large scale flow and transport models in subsurface. In particular, pore-scale changes (e.g., due to phase transitions or reactive transport ) impact the porescale flow patterns, and impact the crucial large-scale flow parameters such as porosity and permeability. When numerically upscaling pore-scale results, it is essential to understand how different means of solving pore-scale flow impact said upscaled results. In this talk, we present ongoing research into this problem, including the choice of numerical discretization, and the particular software implementation. Since transport models require that a conservative velocity field is used, we discuss also the importance of projecting velocity to a conservative field. We show examples of pore-scale flow solutions and of the coupled transport both at the pore-scale and at the Darcy scale. We also discuss different transport solvers (Eulerian and Lagrangian) and some common computational pitfalls.