Be noisy when API is in a coremod. It'll never work and modders should realize that fact.

src/main/java/net/minecraftforge/fml/common/Loader.java

@@ -639,7 +639,7 @@ public class Loader
         return "8.0.99.99";
     }
 
-    public ClassLoader getModClassLoader()
+    public ModClassLoader getModClassLoader()
     {
         return modClassLoader;
     }

src/main/java/net/minecraftforge/fml/common/ModAPIManager.java

@@ -90,6 +90,9 @@ public class ModAPIManager {
 
         public void validate(String providedAPI, String apiOwner, String apiVersion)
         {
+            if (Loader.instance().getModClassLoader().containsSource(this.getSource())) {
+                FMLLog.bigWarning("The API %s from source %s is loaded from an incompatible classloader. THIS WILL NOT WORK!", providedAPI, this.getSource().getAbsolutePath());
+            }
             // TODO Compare this annotation data to the one we first found. Maybe barf if there is inconsistency?
         }
 

src/main/java/net/minecraftforge/fml/common/ModClassLoader.java

@@ -19,6 +19,7 @@ import java.net.URISyntaxException;
 import java.net.URL;
 import java.net.URLClassLoader;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Set;
 
@@ -30,6 +31,7 @@ import net.minecraftforge.fml.common.discovery.ASMDataTable;
 import org.apache.logging.log4j.Level;
 
 import com.google.common.collect.ImmutableList;
+import com.google.common.collect.Lists;
 
 /**
  * A simple delegating class loader used to load mods into the system
@@ -42,6 +44,7 @@ public class ModClassLoader extends URLClassLoader
 {
     private static final List<String> STANDARD_LIBRARIES = ImmutableList.of("jinput.jar", "lwjgl.jar", "lwjgl_util.jar", "rt.jar");
     private LaunchClassLoader mainClassLoader;
+    private List<File> sources;
 
     public ModClassLoader(ClassLoader parent) {
         super(new URL[0], null);
@@ -52,6 +55,7 @@ public class ModClassLoader extends URLClassLoader
     {
         URL url = modFile.toURI().toURL();
         mainClassLoader.addURL(url);
+        this.sources.add(modFile);
     }
 
     @Override
@@ -148,4 +152,20 @@ public class ModClassLoader extends URLClassLoader
         modAPI.initTable(dataTable);
         return modAPI;
     }
+
+    List<URL> parentURLs = null;
+    public boolean containsSource(File source)
+    {
+        if (parentURLs == null) {
+            parentURLs = Arrays.asList(mainClassLoader.getURLs());
+        }
+        try
+        {
+            return parentURLs.contains(source.toURI().toURL());
+        } catch (MalformedURLException e)
+        {
+            // shouldn't happen
+            return false;
+        }
+    }
 }