with version 1.6.2 of M2E I still get NoSuchElementException after the project is refreshed if maven-bundle-plugin is present. This error appeared with the version 1.6.0. I saw that there were issues with the same (or very similar) stacktrace that were solved in previous versions. The exception disappears if I edit the pom file and save it.
Execution m2e-tycho:default-bundle:manifest of goal org.apache.felix:maven-bundle-plugin:3.0.0:manifest failed: Unable to load the mojo 'manifest' (or one of its required components) from the plugin 'org.apache.felix:maven-bundle-plugin:3.0.0' (org.apache.felix:maven-bundle-plugin:3.0.0:bundle:default-bundle:package)
org.apache.maven.plugin.PluginExecutionException: Execution m2e-tycho:default-bundle:manifest of goal org.apache.felix:maven-bundle-plugin:3.0.0:manifest failed: Unable to load the mojo 'manifest' (or one of its required components) from the plugin 'org.apache.felix:maven-bundle-plugin:3.0.0'
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:153)
	at org.eclipse.m2e.core.internal.embedder.MavenImpl.execute(MavenImpl.java:331)
	at org.eclipse.m2e.core.internal.embedder.MavenImpl$11.call(MavenImpl.java:1362)
	at org.eclipse.m2e.core.internal.embedder.MavenImpl$11.call(MavenImpl.java:1)
	at org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.executeBare(MavenExecutionContext.java:176)
	at org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute(MavenExecutionContext.java:112)
	at org.eclipse.m2e.core.internal.embedder.MavenImpl.execute(MavenImpl.java:1360)
	at org.eclipse.m2e.core.project.configurator.MojoExecutionBuildParticipant.build(MojoExecutionBuildParticipant.java:52)
	at org.sonatype.tycho.m2e.internal.AbstractMavenBundlePluginProjectConfigurator$1.build(AbstractMavenBundlePluginProjectConfigurator.java:131)
	at org.eclipse.m2e.core.internal.builder.MavenBuilderImpl.build(MavenBuilderImpl.java:137)
	at org.eclipse.m2e.core.internal.builder.MavenBuilder$1.method(MavenBuilder.java:172)
	at org.eclipse.m2e.core.internal.builder.MavenBuilder$1.method(MavenBuilder.java:1)
	at org.eclipse.m2e.core.internal.builder.MavenBuilder$BuildMethod$1$1.call(MavenBuilder.java:115)
	at org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.executeBare(MavenExecutionContext.java:176)
	at org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute(MavenExecutionContext.java:112)
	at org.eclipse.m2e.core.internal.builder.MavenBuilder$BuildMethod$1.call(MavenBuilder.java:105)
	at org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.executeBare(MavenExecutionContext.java:176)
	at org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute(MavenExecutionContext.java:151)
	at org.eclipse.m2e.core.internal.embedder.MavenExecutionContext.execute(MavenExecutionContext.java:99)
	at org.eclipse.m2e.core.internal.builder.MavenBuilder$BuildMethod.execute(MavenBuilder.java:86)
	at org.eclipse.m2e.core.internal.builder.MavenBuilder.build(MavenBuilder.java:200)
	at org.eclipse.core.internal.events.BuildManager$2.run(BuildManager.java:734)
	at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
	at org.eclipse.core.internal.events.BuildManager.basicBuild(BuildManager.java:205)
	at org.eclipse.core.internal.events.BuildManager.basicBuild(BuildManager.java:245)
	at org.eclipse.core.internal.events.BuildManager$1.run(BuildManager.java:300)
	at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42)
	at org.eclipse.core.internal.events.BuildManager.basicBuild(BuildManager.java:303)
	at org.eclipse.core.internal.events.BuildManager.basicBuildLoop(BuildManager.java:359)
	at org.eclipse.core.internal.events.BuildManager.build(BuildManager.java:382)
	at org.eclipse.core.internal.events.AutoBuildJob.doBuild(AutoBuildJob.java:144)
	at org.eclipse.core.internal.events.AutoBuildJob.run(AutoBuildJob.java:235)
	at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
Caused by: org.apache.maven.plugin.PluginContainerException: Unable to load the mojo 'manifest' (or one of its required components) from the plugin 'org.apache.felix:maven-bundle-plugin:3.0.0'
	at org.apache.maven.plugin.internal.DefaultMavenPluginManager.getConfiguredMojo(DefaultMavenPluginManager.java:579)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:121)
	... 32 more
Caused by: org.codehaus.plexus.component.repository.exception.ComponentLookupException: java.util.NoSuchElementException
      role: org.apache.maven.plugin.Mojo
  roleHint: org.apache.felix:maven-bundle-plugin:3.0.0:manifest
	at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:267)
	at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:255)
	at org.apache.maven.plugin.internal.DefaultMavenPluginManager.getConfiguredMojo(DefaultMavenPluginManager.java:546)
	... 33 more
Caused by: java.util.NoSuchElementException
	at org.eclipse.sisu.plexus.RealmFilteredBeans$FilteredItr.next(RealmFilteredBeans.java:118)
	at org.eclipse.sisu.plexus.RealmFilteredBeans$FilteredItr.next(RealmFilteredBeans.java:1)
	at org.eclipse.sisu.plexus.DefaultPlexusBeans$Itr.next(DefaultPlexusBeans.java:76)
	at org.eclipse.sisu.plexus.DefaultPlexusBeans$Itr.next(DefaultPlexusBeans.java:1)
	at org.codehaus.plexus.DefaultPlexusContainer.lookup(DefaultPlexusContainer.java:263)
	... 35 more