reproduced.rb

# frozen_string_literal: true
require 'torque-postgresql'

require 'byebug'
require "active_record"
require "minitest/autorun"
require "logger"

ActiveRecord::Base.establish_connection(
  adapter:  "postgresql",
  database: "test",
  encoding: "unicode",
  host:     "localhost",
  port:     "5432",
  password: "12345",
  username: "test")

ActiveRecord::Schema.define do
  drop_table "employees", if_exists: true
  drop_table "projects", if_exists: true
  drop_table "departments", if_exists: true

  create_table "employees" do |t|
    t.string "name"
    t.timestamps
  end

  create_table "projects" do |t|
    t.string "title"
    t.timestamps
  end
  
  # This reproduces the issue
  execute "alter table projects add column employees_ids integer[] default '{}'::integer[]"

  create_table "departments" do |t|
    t.string "name"
    t.integer "project_id"
    t.timestamps
  end

end


class Employee < ActiveRecord::Base
end

class Department < ActiveRecord::Base
  after_initialize :do_something, if: :new_record?
  belongs_to :project

  def do_something
    puts "\n[Department] after_initialize called"
    puts "[Department] after_initialize #{self.project&.employees&.count}"
    puts ""
  end
end

class Project < ActiveRecord::Base
  belongs_to_many :employees, foreign_key: "employees_ids"

  validates_presence_of :departments

  has_many :departments
end

#ActiveRecord::Base.logger = Logger.new(STDOUT)

class BugTest < Minitest::Test
  def test_new
    employee = Employee.create!

    project = Project.new(employees: [employee])
    project.departments << Department.new(project: project)

    project.save!

    assert_equal 1, project.employees.count
    assert_equal 1, project.employees_ids.count
  end
end

torque_bug.rb

# frozen_string_literal: true
require 'torque-postgresql'

require 'byebug'
require "active_record"
require "minitest/autorun"
require "logger"

ActiveRecord::Base.establish_connection(
  adapter:  "postgresql",
  database: "test",
  encoding: "unicode",
  host:     "localhost",
  port:     "5432",
  password: "12345",
  username: "test")

ActiveRecord::Schema.define do
  drop_table "employees", if_exists: true
  drop_table "projects", if_exists: true
  drop_table "departments", if_exists: true

  create_table "employees" do |t|
    t.string "name"
    t.timestamps
  end

  create_table "projects" do |t|
    t.bigint "employees_ids", array: true
    t.string "title"
    t.timestamps
  end

  create_table "departments" do |t|
    t.string "name"
    t.integer "project_id"
    t.timestamps
  end

end


class Employee < ActiveRecord::Base
end

class Department < ActiveRecord::Base
  after_initialize :do_something, if: :new_record?
  belongs_to :project

  def do_something
    puts "\n[Department] after_initialize called"
    puts "[Department] after_initialize #{self.project&.employees&.count}"
    puts ""
  end
end

class Project < ActiveRecord::Base
  belongs_to_many :employees, foreign_key: "employees_ids"

  validates_presence_of :departments

  has_many :departments
end

#ActiveRecord::Base.logger = Logger.new(STDOUT)

class BugTest < Minitest::Test
  def test_new
    employee = Employee.create!

    project = Project.new(employees: [employee])
    project.departments << Department.new(project: project)

    project.save!

    assert_equal 1, project.employees.count
    assert_equal 1, project.employees_ids.count
  end
end