Run the following:

---%<---
import java.io.IOException;
import java.net.URI;
import java.util.Collections;
import java.util.Set;
import javax.annotation.processing.AbstractProcessor;
import javax.annotation.processing.RoundEnvironment;
import javax.annotation.processing.SupportedAnnotationTypes;
import javax.annotation.processing.SupportedSourceVersion;
import javax.lang.model.SourceVersion;
import javax.lang.model.element.TypeElement;
import javax.tools.JavaCompiler;
import javax.tools.JavaCompiler.CompilationTask;
import javax.tools.JavaFileObject;
import javax.tools.SimpleJavaFileObject;
import javax.tools.StandardLocation;
import javax.tools.ToolProvider;
@SupportedAnnotationTypes("*")
@SupportedSourceVersion(SourceVersion.RELEASE_6)
public class JSR269FilerBug extends AbstractProcessor {
    public boolean process(Set<? extends TypeElement> annotations, RoundEnvironment roundEnv) {
        if (!roundEnv.processingOver()) {
            try {
                processingEnv.getFiler().createResource(StandardLocation.CLASS_OUTPUT, "", "META-INF/.something1");
                processingEnv.getFiler().createResource(StandardLocation.CLASS_OUTPUT, "", ".something2");
            } catch (Exception x) {
                x.printStackTrace();
            }
        }
        return true;
    }
    public static void main(String[] args) {
        JavaCompiler compiler = ToolProvider.getSystemJavaCompiler();
        JavaFileObject file = new SimpleJavaFileObject(URI.create("no://where"), JavaFileObject.Kind.SOURCE) {
            @Override public CharSequence getCharContent(boolean ignoreEncodingErrors) throws IOException {
                return "class X {}";
            }
        };
        CompilationTask task = compiler.getTask(null, null, null, null, null, Collections.singleton(file));
        task.setProcessors(Collections.singleton(new JSR269FilerBug()));
        task.call();
    }
}
---%<---

On JDK 6 I get:

---%<---
java.lang.IllegalArgumentException: relativeName is invalid
        at com.sun.tools.javac.util.DefaultFileManager.getFileForOutput(DefaultFileManager.java:1050)
        at com.sun.tools.javac.processing.JavacFiler.createResource(JavacFiler.java:404)
        at JSR269FilerBug.process(JSR269FilerBug.java:24)
        at com.sun.tools.javac.processing.JavacProcessingEnvironment.callProcessor(JavacProcessingEnvironment.java:624)
        at com.sun.tools.javac.processing.JavacProcessingEnvironment.discoverAndRunProcs(JavacProcessingEnvironment.java:553)
        at com.sun.tools.javac.processing.JavacProcessingEnvironment.doProcessing(JavacProcessingEnvironment.java:698)
        at com.sun.tools.javac.main.JavaCompiler.processAnnotations(JavaCompiler.java:981)
        at com.sun.tools.javac.main.JavaCompiler.compile(JavaCompiler.java:727)
        at com.sun.tools.javac.main.Main.compile(Main.java:353)
        at com.sun.tools.javac.api.JavacTaskImpl.call(JavacTaskImpl.java:115)
        at JSR269FilerBug.main(JSR269FilerBug.java:40)
---%<---

(Similar on JDK 7, though the class names have changed a little.)

In other words, "META-INF/.something1" is accepted as a resource name to create, but ".something2" is rejected. This is contrary to the Filer specification:

"A relative name is a non-null, non-empty sequence of path segments separated by '/'; '.' and '..' are invalid path segments."

Here the '.' is only part of a larger path segment.