I've similar problem which was mentioned over there. I'm using mvn clean compile site command and my versions are:
- cobertura.version: 2.5.1
 - findbugs.version: 2.5.1
 - maven-compiler-plugin.version: 2.5.1
 - maven.version: 2.2.1
 - java.version: 1.6.0_45
 
The error I get is:
java.lang.ClassCastException: org.apache.xerces.parsers.XIncludeAwareParserConfiguration cannot be cast to org.apache.xerces.xni.parser.XMLParserConfi
guration
        at org.apache.xerces.parsers.SAXParser.<init>(Unknown Source)
        at org.apache.xerces.parsers.SAXParser.<init>(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.<init>(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserImpl.<init>(Unknown Source)
        at org.apache.xerces.jaxp.SAXParserFactoryImpl.newSAXParser(Unknown Source)
        at org.apache.tools.ant.util.JAXPUtils.newSAXParser(JAXPUtils.java:215)
        at org.apache.tools.ant.util.JAXPUtils.getNamespaceXMLReader(JAXPUtils.java:172)
        at org.apache.tools.ant.helper.ProjectHelper2.parse(ProjectHelper2.java:273)
        at org.apache.tools.ant.helper.ProjectHelper2.parseUnknownElement(ProjectHelper2.java:131)
        at org.apache.tools.ant.helper.ProjectHelper2.parseAntlibDescriptor(ProjectHelper2.java:111)
        at org.apache.tools.ant.taskdefs.Antlib.createAntlib(Antlib.java:91)
        at org.apache.tools.ant.taskdefs.Definer.loadAntlib(Definer.java:440)
        at org.apache.tools.ant.taskdefs.Definer.execute(Definer.java:292)
        at org.apache.tools.ant.ComponentHelper.checkNamespace(ComponentHelper.java:869)
        at org.apache.tools.ant.ComponentHelper.getDefinition(ComponentHelper.java:308)
        at org.apache.tools.ant.ComponentHelper.createComponent(ComponentHelper.java:285)
        at org.apache.tools.ant.ComponentHelper.createComponent(ComponentHelper.java:264)
        at org.apache.tools.ant.UnknownElement.makeObject(UnknownElement.java:417)
        at org.apache.tools.ant.UnknownElement.maybeConfigure(UnknownElement.java:163)
        at groovy.util.AntBuilder.nodeCompleted(AntBuilder.java:181)
        at groovy.util.BuilderSupport.doInvokeMethod(BuilderSupport.java:147)
        at groovy.util.AntBuilder.doInvokeMethod(AntBuilder.java:149)
        at groovy.util.BuilderSupport.invokeMethod(BuilderSupport.java:64)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:756)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:730)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodN(ScriptBytecodeAdapter.java:170)
        at org.codehaus.mojo.findbugs.FindBugsMojo.executeFindbugs(FindBugsMojo.groovy:1004)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:86)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:230)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:912)
        at org.codehaus.groovy.runtime.ScriptBytecodeAdapter.invokeMethodOnCurrentN(ScriptBytecodeAdapter.java:78)
        at org.codehaus.mojo.findbugs.FindBugsMojo.executeReport(FindBugsMojo.groovy:640)
        at org.apache.maven.reporting.AbstractMavenReport.generate(AbstractMavenReport.java:190)
        at org.apache.maven.reporting.AbstractMavenReport.generate(AbstractMavenReport.java:144)
        at org.apache.maven.plugins.site.ReportDocumentRenderer.renderDocument(ReportDocumentRenderer.java:164)
        at org.apache.maven.doxia.siterenderer.DefaultSiteRenderer.renderModule(DefaultSiteRenderer.java:330)
        at org.apache.maven.doxia.siterenderer.DefaultSiteRenderer.render(DefaultSiteRenderer.java:134)
        at org.apache.maven.plugins.site.SiteMojo.renderLocale(SiteMojo.java:158)
        at org.apache.maven.plugins.site.SiteMojo.execute(SiteMojo.java:120)
        at org.apache.maven.plugin.DefaultPluginManager.executeMojo(DefaultPluginManager.java:490)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoals(DefaultLifecycleExecutor.java:694)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalWithLifecycle(DefaultLifecycleExecutor.java:556)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoal(DefaultLifecycleExecutor.java:535)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeGoalAndHandleFailures(DefaultLifecycleExecutor.java:387)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.executeTaskSegments(DefaultLifecycleExecutor.java:348)
        at org.apache.maven.lifecycle.DefaultLifecycleExecutor.execute(DefaultLifecycleExecutor.java:180)
        at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:328)
        at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:138)
        at org.apache.maven.cli.MavenCli.main(MavenCli.java:362)
        at org.apache.maven.cli.compat.CompatibleMain.main(CompatibleMain.java:60)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
        at java.lang.reflect.Method.invoke(Method.java:597)
        at org.codehaus.classworlds.Launcher.launchEnhanced(Launcher.java:315)
        at org.codehaus.classworlds.Launcher.launch(Launcher.java:255)
        at org.codehaus.classworlds.Launcher.mainWithExitCode(Launcher.java:430)
        at org.codehaus.classworlds.Launcher.main(Launcher.java:375)