Various exceptions appear in the CQ error.log when you apply the CQ 5.6.1 Security Service Pack. For example:
ERROR [OsgiInstallerImpl] org.apache.aries.jmx.whiteboard.MBeanHolder register: Failure registering MBeanorg.apache.jackrabbit.vault.packaging.impl.PackageManagerMBeanImpl@185c7b8 javax.management.InstanceAlreadyExistsException: com.adobe.granite.packaging:type=manage
ERROR [127.0.0.1  PUT /libs/sling/topology/connector.af8050f4-e48a-42cc-bf40-3d4c86a297fd.json HTTP/1.1] org.apache.sling.servlets.resolver.internal.SlingServletResolver Original error class java.io.IOException java.io.IOException: Unable to get component of class 'interface org.apache.sling.rewriter.Generator' with type 'htmlparser'.
ERROR [FelixDispatchQueue] com.day.cq.dam.cq-dam-handler FrameworkEvent ERROR (org.osgi.framework.ServiceException: Service factory returned null.) org.osgi.framework.ServiceException: Service factory returned null.
These errors observed during the installation of 5.6.1 Security Service Pack, are transient in nature. Adobe Engineering as reviewed these exceptions, and no side-effect has been observed during the testing of 5.6.1 Security Service Pack. These exceptions occur due to the dynamic nature of runtime environment as some of the core services (that is,repository) are still starting up, while other components are trying to use those. These errors don't persist once the installation of Security Service Pack finishes.
Since the list of exceptions that we know is not exhaustive, you could see different exceptions reported. If you are getting the exceptions during the Security SP installation, you should observe the system until all bundles come to the running state. All the transient exceptions go away. If the issue persists, contact Adobe Customer Care.
Make a backup of the system before applying any updates.