Using the following code I get an error regarding an invalid key, because it contains a dot, on Mongoid v5.1.4 + mongo-ruby-driver v2.3.0 when running `rake db:mongoid:create_indexes`.
Downgrading to mongo-ruby-driver v.2.2.x resolved the issue.
Also works in mongoid 4.x.

class Post
  include Mongoid::Document

  embeds_many :comments
  index({ 'comment.ref' => 1 })
end

class Comment
  include Mongoid::Document

  field :ref, type: String
  embedded_in :post
end

I can provide you with the full stacktrace later if required.

Cheers!