Despite significant progress, malapposed or overlapped stents are a complication that affects daily percutaneous coronary intervention (PCI) procedures. These malapposed stents affect blood flow and create a micro re-circulatory environment. These disturbances are often associated with a change in Wall Shear Stress (WSS), Time-averaged WSS (TAWSS), relative residence time (RRT) and oscillatory character of WSS and disrupt the delicate balance of vascular biology, providing a possible source of thrombosis and restenosis. In this study, 2D axisymmetric parametric computational fluid dynamics (CFD) simulations were performed to systematically analyze the hemodynamic effects of malapposition and stent overlap for two types of stents (drug-eluting stent and a bioresorbable stent). The results of the modeling are mainly analyzed using streamlines, TAWSS, oscillatory shear index (OSI) and RRT. The risks of restenosis and thrombus are evaluated according to commonly accepted thresholds for TAWSS and OSI. The small malapposition distances (MD) cause both low TAWSS and high OSI, which are potential adverse outcomes. The region of low OSI decrease with MD. Overlap configurations produce areas with low WSS and high OSI. The affected lengths are relatively insensitive to the overlap distance. The effects of strut size are even more sensitive and adverse for overlap configurations compared to a well-applied stent.