diff --git a/dowhy/gcm/divergence.py b/dowhy/gcm/divergence.py
index 88ddf4e74..59b141c15 100644
--- a/dowhy/gcm/divergence.py
+++ b/dowhy/gcm/divergence.py
@@ -61,7 +61,7 @@ def estimate_kl_divergence_continuous_knn(
     # Making sure that X and Y have no overlapping values, which would lead to a distance of 0 with k=1 and, thus, to
     # a division by zero.
     if remove_common_elements:
-        X = setdiff2d(X, Y, assume_unique=True)
+        X = setdiff2d(X, Y, assume_unique=False)
         if X.shape[0] < k + 1:
             # All elements are equal (or at least less than k samples are different)
             return 0