You don't describe what the broken behaviour is or provide an example project, which makes it hard to fix.
Note "MavenProject.getArtifacts" should always returns both direct and transitive dependencies both in Maven 2 and Maven 3, but there may be a difference between them wrt. which dependencies are resolved at the time of provisioning. This is because Maven 3 honours the @requiresDependencyResolution mojo setting and makes sure the resolved set matches the request, whereas with Maven 2 the visible set of resolved dependencies could vary depending on what plugins ran before your plugin.
Regardless of the difference between Maven 2 and Maven 3, there was an explicit request to look for bundles in transitive dependencies https://ops4j1.jira.com/browse/PAXCONSTRUCT-123 which means the plugin is currently "working as designed".
Whether we should provide a switch to only look at direct (non-transitive) dependencies is of course another question...