diff --git a/pmd-core/src/main/java/net/sourceforge/pmd/cpd/CpdAnalysis.java b/pmd-core/src/main/java/net/sourceforge/pmd/cpd/CpdAnalysis.java
index d9b8f452b3..34497c47f4 100644
--- a/pmd-core/src/main/java/net/sourceforge/pmd/cpd/CpdAnalysis.java
+++ b/pmd-core/src/main/java/net/sourceforge/pmd/cpd/CpdAnalysis.java
@@ -24,6 +24,7 @@ import net.sourceforge.pmd.lang.Language;
 import net.sourceforge.pmd.lang.LanguagePropertyBundle;
 import net.sourceforge.pmd.lang.ast.FileAnalysisException;
 import net.sourceforge.pmd.lang.ast.LexException;
+import net.sourceforge.pmd.lang.ast.impl.javacc.MalformedSourceException;
 import net.sourceforge.pmd.lang.document.FileCollector;
 import net.sourceforge.pmd.lang.document.FileId;
 import net.sourceforge.pmd.lang.document.InternalApiBridge;
@@ -171,7 +172,7 @@ public final class CpdAnalysis implements AutoCloseable {
                     int newTokens = doTokenize(textDocument, tokenizers.get(textFile.getLanguageVersion().getLanguage()), tokens);
                     numberOfTokensPerFile.put(textDocument.getFileId(), newTokens);
                     listener.addedFile(1);
-                } catch (LexException | IOException e) {
+                } catch (LexException | IOException | MalformedSourceException e) {
                     if (e instanceof FileAnalysisException) { // NOPMD
                         ((FileAnalysisException) e).setFileId(textFile.getFileId());
                     }
diff --git a/pmd-core/src/main/java/net/sourceforge/pmd/lang/document/BaseMappedDocument.java b/pmd-core/src/main/java/net/sourceforge/pmd/lang/document/BaseMappedDocument.java
index 55daae33ce..be92385faa 100644
--- a/pmd-core/src/main/java/net/sourceforge/pmd/lang/document/BaseMappedDocument.java
+++ b/pmd-core/src/main/java/net/sourceforge/pmd/lang/document/BaseMappedDocument.java
@@ -68,6 +68,9 @@ abstract class BaseMappedDocument implements TextDocument {
      * @return Input region
      */
     protected @NonNull TextRegion inputRegion(TextRegion outputRegion) {
+        if (outputRegion.isEmpty()) {
+            return TextRegion.caretAt(inputOffset(outputRegion.getStartOffset(), false));
+        }
         return TextRegion.fromBothOffsets(inputOffset(outputRegion.getStartOffset(), true),
                                           inputOffset(outputRegion.getEndOffset(), false));
     }