diff --git a/engine/runtime-compiler/src/main/java/org/enso/compiler/pass/IRHelpers.java b/engine/runtime-compiler/src/main/java/org/enso/compiler/pass/IRHelpers.java
new file mode 100644
index 000000000000..a536eab89813
--- /dev/null
+++ b/engine/runtime-compiler/src/main/java/org/enso/compiler/pass/IRHelpers.java
@@ -0,0 +1,79 @@
+package org.enso.compiler.pass;
+
+import java.util.ArrayDeque;
+import java.util.HashSet;
+import java.util.IdentityHashMap;
+import java.util.Set;
+import org.enso.compiler.core.IR;
+import org.enso.scala.wrapper.ScalaConversions;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+final class IRHelpers {
+  private static final Logger LOG = LoggerFactory.getLogger(IRHelpers.class);
+  private static HashSet<Integer> reportedIdentityHashCodes;
+
+  private IRHelpers() {}
+
+  /**
+   * Processes whole IR subtree to find (top most) elements that are referenced multiple times.
+   *
+   * @param root the root of IR tree to process
+   * @return set of IR elements that appear at least twice
+   */
+  private static Set<IR> findTopMostDuplicates(IR root) {
+    var foundIR = new IdentityHashMap<IR, Integer>();
+    var irToProcess = new ArrayDeque<IR>();
+    irToProcess.add(root);
+    while (!irToProcess.isEmpty()) {
+      var ir = irToProcess.remove();
+      if (foundIR.containsKey(ir)) {
+        foundIR.put(ir, 1);
+      } else {
+        foundIR.put(ir, 0);
+        irToProcess.addAll(ScalaConversions.asJava(ir.children()));
+      }
+    }
+    var it = foundIR.entrySet().iterator();
+    while (it.hasNext()) {
+      if (it.next().getValue() == 0) {
+        it.remove();
+      }
+    }
+    return foundIR.keySet();
+  }
+
+  static <IRType extends IR> IRType checkDuplicates(String msg, IRType ir) {
+    var duplicates = findTopMostDuplicates(ir);
+    if (duplicates.isEmpty()) {
+      return ir;
+    } else {
+      if (reportedIdentityHashCodes == null) {
+        reportedIdentityHashCodes = new HashSet<>();
+      }
+      var all = ir.preorder();
+      for (var dupl : duplicates) {
+        if (!reportedIdentityHashCodes.add(System.identityHashCode(dupl))) {
+          continue;
+        }
+        LOG.error("Duplicate found after " + msg + ": " + toString(dupl));
+        all.foreach(
+            e -> {
+              if (e.children().contains(dupl)) {
+                LOG.error("  referenced by " + toString(e));
+              }
+              return null;
+            });
+      }
+    }
+    return ir;
+  }
+
+  private static String toString(IR ir) {
+    return ir.getClass().getName()
+        + "@"
+        + Integer.toHexString(System.identityHashCode(ir))
+        + ":"
+        + ir.showCode();
+  }
+}
diff --git a/engine/runtime-compiler/src/main/scala/org/enso/compiler/pass/PassManager.scala b/engine/runtime-compiler/src/main/scala/org/enso/compiler/pass/PassManager.scala
index 9c643deeb200..08bc38d690df 100644
--- a/engine/runtime-compiler/src/main/scala/org/enso/compiler/pass/PassManager.scala
+++ b/engine/runtime-compiler/src/main/scala/org/enso/compiler/pass/PassManager.scala
@@ -173,7 +173,12 @@ class PassManager(
         pendingMiniPasses.clear()
         if (combinedPass != null) {
           logger.trace("  flushing pending mini pass: {}", combinedPass)
-          miniPassCompile(combinedPass, in)
+          val res = miniPassCompile(combinedPass, in)
+          IRHelpers.checkDuplicates(
+            "Flushing mini passes: " + combinedPass,
+            res
+          )
+          res
         } else {
           in
         }
@@ -220,7 +225,8 @@ class PassManager(
               "  mega running: {}",
               megaPass
             )
-            megaPassCompile(megaPass, flushedIR, context)
+            val res = megaPassCompile(megaPass, flushedIR, context)
+            IRHelpers.checkDuplicates("" + megaPass.getClass().getName(), res)
         }
     }
 
diff --git a/engine/runtime-compiler/src/main/scala/org/enso/compiler/pass/desugar/Imports.scala b/engine/runtime-compiler/src/main/scala/org/enso/compiler/pass/desugar/Imports.scala
index 51cfcc0588b2..1188afe76c96 100644
--- a/engine/runtime-compiler/src/main/scala/org/enso/compiler/pass/desugar/Imports.scala
+++ b/engine/runtime-compiler/src/main/scala/org/enso/compiler/pass/desugar/Imports.scala
@@ -50,7 +50,8 @@ case object Imports extends IRPass {
             val parts = newName.parts
             if (parts.length == 2) {
               i.copy(
-                name = newName.copy(parts = parts :+ mainModuleName),
+                name =
+                  newName.copy(parts = parts :+ mainModuleName.duplicate()),
                 rename = computeRename(
                   i.rename,
                   i.onlyNames.nonEmpty || i.isAll,
diff --git a/lib/scala/logging-truffle-connector/src/main/scala/org/enso/truffleloggerwrapper/TruffleLoggerWrapper.scala b/lib/scala/logging-truffle-connector/src/main/scala/org/enso/truffleloggerwrapper/TruffleLoggerWrapper.scala
index 603eee0b7302..fda39dcd8506 100644
--- a/lib/scala/logging-truffle-connector/src/main/scala/org/enso/truffleloggerwrapper/TruffleLoggerWrapper.scala
+++ b/lib/scala/logging-truffle-connector/src/main/scala/org/enso/truffleloggerwrapper/TruffleLoggerWrapper.scala
@@ -22,8 +22,11 @@ class TruffleLoggerWrapper(name: String, masking: Masking) extends Logger {
 
   override def getName: String = underlying.getName
 
-  private def isEnabled(level: Level): Boolean =
+  private def isEnabled(level: Level): Boolean = try {
     underlying.isLoggable(level)
+  } catch {
+    case _: IllegalStateException => false
+  }
 
   private def log(
     level: Level,