AR bug with circular destroy: I am able to replicate this issue for later release including 4.0.0 for has_many relationship. It's fine for earlier release.

ar-has_many_throught

unless File.exist?('Gemfile')
  File.write('Gemfile', <<-GEMFILE)
    source 'https://rubygems.org'
    gem 'rails', '3.2.12'
    gem 'arel'
    gem 'mysql2'
  GEMFILE

  system 'bundle'
end

require 'bundler'
Bundler.setup(:default)

require 'active_record'
require 'minitest/autorun'
require 'logger'

# This connection will do for database-independent bug reports.
#ActiveRecord::Base.establish_connection(adapter: 'sqlite3', database: ':memory:')
ActiveRecord::Base.establish_connection(adapter: 'mysql2', host: 'localhost', port: '3306', database: 'testing_test')
ActiveRecord::Base.logger = Logger.new(STDOUT)

ActiveRecord::Schema.define do
  unless ActiveRecord::Base.connection.table_exists? 'physicians'
    create_table :physicians do |t|
      t.string :name
      t.timestamps
    end
  end
 
  unless ActiveRecord::Base.connection.table_exists? 'patients'
    create_table :patients do |t|
      t.string :name
      t.timestamps
    end
  end
 
  unless ActiveRecord::Base.connection.table_exists? 'appointments'
    create_table :appointments do |t|
      t.references :patient
      t.references :physician
      t.datetime :appointment_date
      t.timestamps
    end
  end
end

class Physician < ActiveRecord::Base
  has_many :appointments, dependent: :destroy
  has_many :patient, through: :appointment
end

class Appointment < ActiveRecord::Base
  belongs_to :physician
  belongs_to :patient, dependent: :destroy
end

class Patient < ActiveRecord::Base
  has_many :appointments, dependent: :destroy
  has_many :physician, through: :appointment
end

class BugTest < MiniTest::Unit::TestCase
  def test_save_failed
    physician = Physician.create!
    patient = Patient.create!
    appointment = Appointment.create!(physician: physician, patient: patient, appointment_date: Date.today)

    #puts physician.appointments.inspect
    #puts physician.appointments.size.inspect
    #puts physician.appointments(true).empty?.inspect
	
    physician.destroy # here we get a stack level too deep error
    assert physician.destroyed?
  end
end