Mathematical models of epidemiological systems enable investigation of and predictions about potential disease outbreaks. However, commonly used models are often highly simplified representations of incredibly complex systems. Because of these simplifications, the model output, of, say, new cases of a disease over time or when an epidemic will occur, may be inconsistent with the available data. In this case, we must improve the model, especially if we plan to make decisions based on it that could affect human health and safety, but direct improvements are often beyond our reach. In this work, we explore this problem through a case study of the Zika outbreak in Brazil in 2016. We propose an embedded discrepancy operator-a modification to the model equations that requires modest information about the system and is calibrated by all relevant data. We show that the new enriched model demonstrates greatly increased consistency with real data. Moreover, the method is general enough to easily apply to many other mathematical models in epidemiology.