Add a guard clause to avoid creating empty stages

lib/gitlab/ci/pipeline/chain/populate.rb

@@ -19,6 +19,9 @@ module Gitlab
             pipeline.stage_seeds.each do |seed|
               seed.user = current_user
+              # TODO, this needs specs, no test coverage
+              next unless seed.included?
+
               pipeline.stages << seed.to_resource
             end