The plugin is probably getting the resources directly from the DB with $modx->getCollection(), which would bypass the permission system. You would probably have to modify the plugin.
If you just want the resources for the current context, it would be relatively simple to add that as a criterion to the getCollection() call.
The current context is available with:
$currentContext = $modx->context->get('key');
and adding 'context_key' => $currentContext as a criterion for getCollection() would get you only resources from that context. Feel free to paste the code used with getCollection() here.
If you need to check the user permissions for individual documents, it's more complicated.