Physics-based numerical modeling of earthquake source processes strives to predict quantities of interest for seismic hazard, such as the probability of an earthquake rupture jumping between fault segments. How to assess the predictive power of numerical models remains a topic of ongoing debate. Here, we investigate how sensitive the outcomes of numerical simulations of sequences of earthquakes and aseismic slip are to choices in numerical discretization and treatment of inertial effects, using a simplified 2-D crustal fault model with two co-planar segments separated by a creeping barrier. Our simulations demonstrate that simplifying inertial effects and using oversized cells significantly affects the resulting earthquake sequences, including the rate of two-segment ruptures. We find that fault models with different properties and modeling assumptions can produce similar frequency-magnitude statistics and static stress drops but have different rates of two-segment ruptures. For sufficiently long faults, we find that long-term sequences of events can substantially differ even among simulations that are well resolved by standard considerations. In such simulations, some outcomes, such as static stress drops, are similar among adequately resolved simulations, whereas others, such as the rate of two-segment ruptures, can be highly sensitive to numerical procedures and modeling assumptions. While it is possible that the response of models with additional ingredients -Realistic fault geometry, fluid effects, etc. -Would be less sensitive to numerical procedures, our results emphasize the need to examine the potential dependence of simulation outcomes on the modeling procedures and resolution, particularly when assessing their predictive value for seismic hazard assessment. Plain Language Summary There is growing interest in using computer simulations of long-term earthquake sequences to determine quantities of interest for seismic hazard, such as the probability of an earthquake rupture jumping from one fault segment to another. This is because large earthquakes are rare, hence the need to assess potential future earthquake scenarios through numerical modeling based on all available field observations and knowledge of fault physics. However, the outcomes of numerical simulations can depend on choices in modeling approximations and numerical procedures. Here, we numerically simulate earthquake sequences in a model with two fault segments separated by a barrier and study how the resulting earthquake sequences depend on common modeling choices. We find that different treatment of the inertial effects and small changes in physical and numerical parameters can result in different simulated long-term sequences, including significant changes in the rate of multisegment ruptures. This is true even when certain properties of the earthquake sequences are similar, such as the earthquake frequency-magnitude statistics and the average stress drop. Our results emphasize the need to examine how simulation outcomes may depend on modeling choices when assessing their predictive value and explore the sensitivity of hazard parameters to model uncertainty.