diff --git a/src/merge_ska_array.rs b/src/merge_ska_array.rs
index ff472a8..ce413f8 100644
--- a/src/merge_ska_array.rs
+++ b/src/merge_ska_array.rs
@@ -342,6 +342,8 @@ where
                 } else {
                     removed += 1;
                 }
+            } else {
+                removed += 1;
             }
         }
         self.variants = filtered_variants;