This study explores the calculation of Reference Discontinuity Factors (RDFs) using the Serpent Monte Carlo code, focusing on the methodology and potential pitfalls. In two-step reactor analyses, consistently generated RDFs are crucial for aligning homogeneous nodal diffusion results with the reference heterogeneous transport solution. However, the Serpent internal diffusion solver, based on the Analytic Function Expansion Nodal (AFEN) method, may not be compatible with other nodal methods such as the Nodal Expansion Method (NEM). Additionally, the solver can suffer from instabilities, particularly in multi-group calculations, leading to erroneous RDFs. Despite these challenges, Serpent can generate the necessary raw data for RDF calculation, which can be accurately processed using external diffusion solvers. Two numerical examples − a 1D fuel-reflector model and a 2D SMR core model − illustrate the effects of consistent and inconsistent RDFs on simulation accuracy. The study emphasizes the importance of using compatible diffusion solvers and thoroughly assessing RDFs to avoid errors in reactor simulations.