diff --git a/libraries/commonConfiguration.gradle b/libraries/commonConfiguration.gradle
index 84f24981223..e241fefac16 100644
--- a/libraries/commonConfiguration.gradle
+++ b/libraries/commonConfiguration.gradle
@@ -65,12 +65,14 @@ ext.compileJava9Sources = { Project project, String moduleName, Collection<FileC
         it.options.sourcepath = files(java9SourceSet.srcDirs)
 
         doFirst {
-            def moduleFiles = moduleOutputs.collect { it.files }.flatten().join(File.pathSeparator)
+            def moduleFiles = files(*moduleOutputs)
+            def modulePath = project.configurations.compileClasspath.filter { !(it in moduleFiles.files) }
 
             options.compilerArgs = [
-                    '--module-path', project.configurations.compileClasspath.asPath,
-                    '--patch-module', "$moduleName=$moduleFiles"
+                    '--module-path', modulePath.asPath,
+                    '--patch-module', "$moduleName=${moduleFiles.asPath}"
             ]
+
             classpath = files()
         }
     }
diff --git a/libraries/reflect/api/build.gradle b/libraries/reflect/api/build.gradle
index 3090d868520..e04c760ac17 100644
--- a/libraries/reflect/api/build.gradle
+++ b/libraries/reflect/api/build.gradle
@@ -22,7 +22,12 @@ dependencies {
     compileOnly project(':core:util.runtime')
 }
 
-compileJava9Sources(project, 'kotlin.reflect', [sourceSets.main.output, configurations.compileOnly])
+compileJava9Sources(
+        project, 'kotlin.reflect',
+        [sourceSets.main.output, configurations.compileOnly.filter {
+            !it.name.contains("kotlin-stdlib")
+        }]
+)
 
 compileKotlin {
     kotlinOptions {