In this work we study molecular dynamics simulations of symmetric nuclear matter using a semi-classical nucleon interaction model. We show that, at sub-saturation densities and low temperatures, the solutions are non-homogeneous structures reminiscent of the "nuclear pasta" phases expected in Neutron Star Matter simulations, but shaped by artificial aspects of the simulations. We explore different geometries for the periodic boundary conditions imposed on the simulation cell: cube, hexagonal prism and truncated octahedron. We find that different cells may yield different solutions for the same physical conditions (i.e. density and temperature). The particular shape of the solution at a given density can be predicted analitically by energy minimization. We also show that even if this behavior is due to finite size effects, it does not mean that it vanishes for very large systems and it actually is independent of the system size: The system size sets the only characteristic length scale for the inhomogeneities.We then include a screened Coulomb interaction, as a model of Neutron Star Matter, and perform simulations in the three cell geometries. In this case, the competition between competing interactions of different range produces the well known nuclear pasta, with (in most cases) several structures per cell. However, we find that the results are affected by finite size in different ways depending on the geometry of the cell. In particular, at the same physical conditions and system size, the hexagonal prism yields a single structure per cell while the cubic and truncated octahedron show consistent results with more than one structure per cell. In this case, the results in every cell are expected to converge for systems much larger than the characteristic length scale that arises from the competing interactions.