Not sure if this is fixable, but we have a supporting rails app, that looks for its data in a main's app db.
So some models have this code:

class User
 store_in collection: 'users', session: 'main_app'
...

These collections are not cleaned by DatabseCleaner. To fix this we need to use:

 config.after(:each) do
 DatabaseCleaner[:mongoid].clean
 Mongoid.session('main_app').collections.each do |collection|
 collection.drop
 end
 end