diff --git a/codegen/apt/src/main/java/io/helidon/codegen/apt/AptContextImpl.java b/codegen/apt/src/main/java/io/helidon/codegen/apt/AptContextImpl.java
index b5247ed926c..db808af3cbf 100644
--- a/codegen/apt/src/main/java/io/helidon/codegen/apt/AptContextImpl.java
+++ b/codegen/apt/src/main/java/io/helidon/codegen/apt/AptContextImpl.java
@@ -145,7 +145,7 @@ private static Optional<ModuleInfo> findModule(Filer filer) {
             try (InputStream in = resource.openInputStream()) {
                 return Optional.of(ModuleInfoSourceParser.parse(in));
             }
-        } catch (IOException ignored) {
+        } catch (Exception ignored) {
             // it is not in sources, let's see if it got generated
         }
         // generated
diff --git a/codegen/apt/src/main/java/io/helidon/codegen/apt/AptTypeInfoFactory.java b/codegen/apt/src/main/java/io/helidon/codegen/apt/AptTypeInfoFactory.java
index 70146921928..7d447a70d19 100644
--- a/codegen/apt/src/main/java/io/helidon/codegen/apt/AptTypeInfoFactory.java
+++ b/codegen/apt/src/main/java/io/helidon/codegen/apt/AptTypeInfoFactory.java
@@ -255,7 +255,13 @@ public static Optional<TypedElementInfo> createTypedElementInfoFromElement(AptCo
                 .throwsChecked(thrownChecked)
                 .parameterArguments(params)
                 .originatingElement(v);
-        AptTypeFactory.createTypeName(v.getEnclosingElement()).ifPresent(builder::enclosingType);
+
+        // To be failure-tolerant, as the ECJ may not provide an enclosing element for a VariableElement.
+        Element enclosingElement = v.getEnclosingElement();
+        if (enclosingElement != null) {
+            AptTypeFactory.createTypeName(enclosingElement).ifPresent(builder::enclosingType);
+        }
+
         Optional.ofNullable(defaultValue).ifPresent(builder::defaultValue);
 
         return mapElement(ctx, builder.build());
diff --git a/codegen/apt/src/main/java/io/helidon/codegen/apt/FilerTextResourceImpl.java b/codegen/apt/src/main/java/io/helidon/codegen/apt/FilerTextResourceImpl.java
index f0cfb8ed4f6..c694c4674f1 100644
--- a/codegen/apt/src/main/java/io/helidon/codegen/apt/FilerTextResourceImpl.java
+++ b/codegen/apt/src/main/java/io/helidon/codegen/apt/FilerTextResourceImpl.java
@@ -76,7 +76,11 @@ public void lines(List<String> newLines) {
     public void write() {
         if (modified) {
             if (originalResource != null) {
-                originalResource.delete();
+                try {
+                    originalResource.delete();
+                } catch (Exception ignored) {
+                    // The resource cannot be deleted, e.g. because ECJ has not implemented this method.
+                }
             }
             try {
                 FileObject newResource = filer.createResource(StandardLocation.CLASS_OUTPUT,
diff --git a/config/metadata/processor/src/main/java/io/helidon/config/metadata/processor/ConfigMetadataHandler.java b/config/metadata/processor/src/main/java/io/helidon/config/metadata/processor/ConfigMetadataHandler.java
index 746f4154bf1..86b5733af80 100644
--- a/config/metadata/processor/src/main/java/io/helidon/config/metadata/processor/ConfigMetadataHandler.java
+++ b/config/metadata/processor/src/main/java/io/helidon/config/metadata/processor/ConfigMetadataHandler.java
@@ -18,6 +18,9 @@
 
 import java.io.IOException;
 import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.lang.annotation.Retention;
+import java.lang.annotation.RetentionPolicy;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.LinkedHashSet;
@@ -49,7 +52,7 @@
 /*
  * This class is separated so javac correctly reports possible errors.
  */
-class  ConfigMetadataHandler {
+class ConfigMetadataHandler {
     /*
      * Configuration metadata file location.
      */
@@ -94,8 +97,7 @@ boolean process(RoundEnvironment roundEnv) {
             return doProcess(roundEnv);
         } catch (Exception e) {
             messager.printMessage(Diagnostic.Kind.ERROR, "Failed to process config metadata annotation processor. "
-                    + toMessage(e));
-            e.printStackTrace();
+                    + stackTraceAsString(e));
             return false;
         }
     }
@@ -210,7 +212,21 @@ private void storeMetadata() {
         }
     }
 
-    private String toMessage(Exception e) {
-        return e.getClass().getName() + ": " + e.getMessage();
+    @Retention(RetentionPolicy.CLASS)
+    private @interface SuppressFBWarnings {
+
+        String[] value() default {};
+
+        String justification() default "";
+    }
+
+    @SuppressFBWarnings(
+            value = "INFORMATION_EXPOSURE_THROUGH_AN_ERROR_MESSAGE",
+            justification = "During compile time this isn't a problem.")
+    private static String stackTraceAsString(Throwable e) {
+        StringWriter sw = new StringWriter();
+        PrintWriter pw = new PrintWriter(sw);
+        e.printStackTrace(pw);
+        return sw.toString();
     }
 }