diff --git a/main/src/main/scala/sbt/Defaults.scala b/main/src/main/scala/sbt/Defaults.scala
index 933b046b4..896c51c07 100644
--- a/main/src/main/scala/sbt/Defaults.scala
+++ b/main/src/main/scala/sbt/Defaults.scala
@@ -745,7 +745,7 @@ object Defaults extends BuildCommon {
         scalaSrcDir.getParentFile / s"${scalaSrcDir.name}-$sv",
         scalaSrcDir.getParentFile / s"${scalaSrcDir.name}-$epochVersion",
         javaSrcDir,
-      )
+      ).distinct
     else
       Seq(scalaSrcDir, javaSrcDir)
   }
diff --git a/sbt-app/src/sbt-test/project/scala3-binary-version/build.sbt b/sbt-app/src/sbt-test/project/scala3-binary-version/build.sbt
new file mode 100644
index 000000000..521755296
--- /dev/null
+++ b/sbt-app/src/sbt-test/project/scala3-binary-version/build.sbt
@@ -0,0 +1,11 @@
+ThisBuild / scalaVersion := "3.0.0"
+
+lazy val check = taskKey[Unit]("check")
+
+lazy val root = project.in(file("."))
+  .settings(
+    check := {
+      val dirs = (Compile / unmanagedSourceDirectories).value
+      assert(dirs == dirs.distinct)
+    }
+  )
diff --git a/sbt-app/src/sbt-test/project/scala3-binary-version/test b/sbt-app/src/sbt-test/project/scala3-binary-version/test
new file mode 100644
index 000000000..15675b169
--- /dev/null
+++ b/sbt-app/src/sbt-test/project/scala3-binary-version/test
@@ -0,0 +1 @@
+> check