diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt
index 37a70e03dc9..088ccd6873a 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinCoreEnvironment.kt
@@ -283,7 +283,7 @@ class KotlinCoreEnvironment private constructor(
 
     fun addKotlinSourceRoots(rootDirs: List<File>) {
         val roots = rootDirs.map { KotlinSourceRoot(it.absolutePath, isCommon = false) }
-        sourceFiles += createSourceFilesFromSourceRoots(configuration, project, roots)
+        sourceFiles += createSourceFilesFromSourceRoots(configuration, project, roots).toSet() - sourceFiles
     }
 
     fun createPackagePartProvider(scope: GlobalSearchScope): JvmPackagePartProvider {
diff --git a/compiler/ir/ir.psi2ir/src/org/jetbrains/kotlin/psi2ir/generators/ModuleGenerator.kt b/compiler/ir/ir.psi2ir/src/org/jetbrains/kotlin/psi2ir/generators/ModuleGenerator.kt
index c8b582789d8..7e056f8813d 100644
--- a/compiler/ir/ir.psi2ir/src/org/jetbrains/kotlin/psi2ir/generators/ModuleGenerator.kt
+++ b/compiler/ir/ir.psi2ir/src/org/jetbrains/kotlin/psi2ir/generators/ModuleGenerator.kt
@@ -46,7 +46,7 @@ class ModuleGenerator(
     fun generateModuleFragment(ktFiles: Collection<KtFile>): IrModuleFragment =
         IrModuleFragmentImpl(context.moduleDescriptor, context.irBuiltIns).also { irModule ->
             val irDeclarationGenerator = DeclarationGenerator(context)
-            ktFiles.mapTo(irModule.files) { ktFile ->
+            ktFiles.toSet().mapTo(irModule.files) { ktFile ->
                 generateSingleFile(irDeclarationGenerator, ktFile)
             }
         }