There is at least one known issue with the version of plexus used:

This is an issue in plexus-resources:1.0-alpha-4 and its classpath resource locator which relied on a bug in the class loaders in Maven 2. Please update the plugin to use the latest plexus-resources version.

The work around for this, for anyone wishing to use Maven3 with Clover2 is:

Independently of an update to the Clover Plugin, you can make the build work right now by overriding the plugin dependency in the POM yourself.

There may be other problems as well.

NB: Maven3 is currently in beta and not one of the versions supported by the Clover2 maven plugin.