active_record_master.rb

unless File.exist?('Gemfile')
  File.write('Gemfile', <<-GEMFILE)
    source 'https://rubygems.org'
    gem 'rails', github: 'rails/rails'
    gem 'arel', github: 'rails/arel'
    gem 'sqlite3'
  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.logger = Logger.new(STDOUT)

ActiveRecord::Schema.define do
  create_table :posts do |t|
  end

  create_table :comments do |t|
    t.integer :post_id
  end
end

class Post < ActiveRecord::Base
  has_many :comments
end

class Comment < ActiveRecord::Base
  belongs_to :post
end

class BugTest < Minitest::Test
  def test_association_stuff
    post = Post.create!
    post.comments << Comment.create!

    assert_equal 1, Post.joins(:comments).uniq.count # Passes
    puts 'Pre-modification count complete'

    attribute_list = Post.attribute_names
    attribute_list.delete('id')

    assert_equal 1, Post.joins(:comments).uniq.count # Fails
  end
end

output

D, [2014-02-24T22:16:35.653465 #4845] DEBUG -- :    (0.3ms)  SELECT DISTINCT COUNT(DISTINCT "posts"."id") FROM "posts" INNER JOIN "comments" ON "comments"."post_id" = "posts"."id"
Pre-modification count complete
D, [2014-02-24T22:16:35.654983 #4845] DEBUG -- :    (0.3ms)  SELECT DISTINCT COUNT(DISTINCT id) FROM "posts" INNER JOIN "comments" ON "comments"."post_id" = "posts"."id"
E, [2014-02-24T22:16:35.655119 #4845] ERROR -- : SQLite3::SQLException: ambiguous column name: id: SELECT DISTINCT COUNT(DISTINCT id) FROM "posts" INNER JOIN "comments" ON "comments"."post_id" = "posts"."id"