diff --git a/paimon-common/src/main/java/org/apache/paimon/utils/Projection.java b/paimon-common/src/main/java/org/apache/paimon/utils/Projection.java
index baf06bf3b634..11c0b6ce4b84 100644
--- a/paimon-common/src/main/java/org/apache/paimon/utils/Projection.java
+++ b/paimon-common/src/main/java/org/apache/paimon/utils/Projection.java
@@ -310,8 +310,11 @@ public Projection complement(int fieldsNumber) {
 
         @Override
         public int[] toTopLevelIndexes() {
-            // todo: fix it usage
-            return Arrays.stream(projection).mapToInt(arr -> arr[0]).toArray();
+            return Arrays.stream(projection)
+                    .map(arr -> arr[0])
+                    .distinct()
+                    .mapToInt(Integer::intValue)
+                    .toArray();
         }
 
         @Override
diff --git a/paimon-spark/paimon-spark-common/src/test/scala/org/apache/paimon/spark/sql/PaimonQueryTest.scala b/paimon-spark/paimon-spark-common/src/test/scala/org/apache/paimon/spark/sql/PaimonQueryTest.scala
index d1169378bcbc..4f5e17fd16f8 100644
--- a/paimon-spark/paimon-spark-common/src/test/scala/org/apache/paimon/spark/sql/PaimonQueryTest.scala
+++ b/paimon-spark/paimon-spark-common/src/test/scala/org/apache/paimon/spark/sql/PaimonQueryTest.scala
@@ -194,6 +194,7 @@ class PaimonQueryTest extends PaimonSparkTestBase {
 
       sql("""
             |SELECT
+            |    course.grade,
             |    name,
             |    course.course_name
             |FROM