In the following example javac crashes on a compilation unit that contains a duplicate annotation declaration, with annotation processing enabled, and if one of the classes being compiled is already present on the classpath.

=== p/Y.java
package p;
class Y {
  @interface A {}
  @interface A {} // error: class A is already defined in class Y
  T t;
}
=== p/T.java
package p;
@Deprecated class T {}
=== P.java
import java.util.Set;
import javax.annotation.processing.AbstractProcessor;
import javax.annotation.processing.RoundEnvironment;
import javax.annotation.processing.SupportedAnnotationTypes;
import javax.lang.model.SourceVersion;
import javax.lang.model.element.TypeElement;

@SupportedAnnotationTypes("*")
public class P extends AbstractProcessor {

  @Override
  public boolean process(Set<? extends TypeElement> annotations, RoundEnvironment roundEnv) {
    return false;
  }

  @Override
  public SourceVersion getSupportedSourceVersion() {
    return SourceVersion.latestSupported();
  }
}
===

javac P.java p/T.java
javac -processor P p/Y.java p/T.java
...
An exception has occurred in the compiler (9.0.1). Please file a bug against the Java compiler via the Java bug reporting page (http://bugreport.java.com) after checking the Bug Database (http://bugs.java.com) for duplicates. Include your program and the following diagnostic in your report. Thank you.
java.lang.AssertionError
        at jdk.compiler/com.sun.tools.javac.util.Assert.error(Assert.java:155)
        at jdk.compiler/com.sun.tools.javac.util.Assert.check(Assert.java:46)
        at jdk.compiler/com.sun.tools.javac.comp.Annotate.lambda$annotateLater$0(Annotate.java:245)
        at jdk.compiler/com.sun.tools.javac.comp.Annotate.flush(Annotate.java:184)
        at jdk.compiler/com.sun.tools.javac.comp.Annotate.unblockAnnotations(Annotate.java:137)
        at jdk.compiler/com.sun.tools.javac.comp.Annotate.enterDone(Annotate.java:150)
        at jdk.compiler/com.sun.tools.javac.main.JavaCompiler.enterDone(JavaCompiler.java:1726)
        at jdk.compiler/com.sun.tools.javac.main.JavaCompiler.enterTrees(JavaCompiler.java:1054)
        at jdk.compiler/com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.java:923)
        at jdk.compiler/com.sun.tools.javac.main.Main.compile(Main.java:302)
        at jdk.compiler/com.sun.tools.javac.main.Main.compile(Main.java:162)
        at jdk.compiler/com.sun.tools.javac.Main.compile(Main.java:57)
        at jdk.compiler/com.sun.tools.javac.Main.main(Main.java:43)

The crash reproduces with:
9.0.1+11
1.8.0_162-ea-b03
1.7.0_80-b15