bug3207.rb

gem 'rails', '3.1.1.rc2'

require 'active_record'

puts "Active Record #{ActiveRecord::VERSION::STRING}"

ActiveRecord::Base.establish_connection(
  :adapter  => 'sqlite3',
  :database => ':memory:'
)

ActiveRecord::Schema.define do
  create_table :apps, :force => true do |t|
  end

  create_table :permissions, :force => true do |t|
    t.integer :app_id
  end
end

class App < ActiveRecord::Base
end

class Permission < ActiveRecord::Base
  belongs_to :app
end

query = Permission.joins(:app)
puts query.to_sql

output.txt

$ ruby ~/Desktop/bug3207.rb
Active Record 3.1.1.rc2
-- create_table(:apps, {:force=>true})
   -> 0.0537s
-- create_table(:permissions, {:force=>true})
   -> 0.0010s
SELECT "permissions".* FROM "permissions" INNER JOIN "apps" ON "apps"."id" = "permissions"."app_id"