Nonparametric two-sample testing is a classical problem in inferential statistics. While modern two-sample tests, such as the edge count test and its variants, can handle multivariate and non-Euclidean data, contemporary gargantuan datasets often exhibit heterogeneity due to the presence of latent subpopulations. Direct application of these tests, without regulating for such heterogeneity, may lead to incorrect statistical decisions. We develop a new nonparametric testing procedure that accurately detects differences between the two samples in the presence of unknown heterogeneity in the data generation process. Our framework handles this latent heterogeneity through a composite null that entertains the possibility that the two samples arise from a mixture distribution with identical component distributions but with possibly different mixing weights. In this regime, we study the asymptotic behavior of weighted edge count test statistic and show that it can be effectively re-calibrated to detect arbitrary deviations from the composite null. For practical implementation we propose a Bootstrapped Weighted Edge Count test which involves a bootstrap-based calibration procedure that can be easily implemented across a wide range of heterogeneous regimes. A comprehensive simulation study and an application to detecting aberrant user behaviors in online games demonstrates the excellent non-asymptotic performance of the proposed test.