Significance Genetic sequencing data of pathogens allow one to quantify the evolutionary rate together with epidemiological dynamics using Bayesian phylodynamic methods. Such tools are particularly useful for obtaining a timely understanding of newly emerging epidemic outbreaks. During the West African Ebola virus disease epidemic, an unusually high evolutionary rate was initially estimated, promoting discussions regarding the potential danger of the strain quickly evolving into an even more dangerous virus. We show here that such high evolutionary rates are not necessarily real but can stem from methodological biases in the analyses. While most analyses of epidemic outbreak data are performed such that these biases may be present, we suggest a solution to overcome these biases in the future.