Issue type:

[ ] question
[x] bug report
[ ] feature request
[ ] documentation issue

Database system/driver:

[ ] cordova
[ ] mongodb
[ ] mssql
[ ] mysql / mariadb
[ ] oracle
[x] postgres
[ ] sqlite
[ ] sqljs
[ ] react-native
[ ] expo

TypeORM version:

[x] latest (0.2.0)
[ ] @next
[ ] 0.x.x (or put your version here)

Steps to reproduce or a small repository showing the problem:

I'm working with a backend where one organisation could have multiple admins (we call them coordinators). One user could be coordinating multiple organisations, so relation between is Many-to-many -relation.

I'm using queryBuilder to delete relations in a following way

const removeCoordinatorFromOrganisation = async (organisationId, userId) => {
  // userId means coordinator
  const organisation = await getConnection.getRepository(Organisation).findOneOrFail(organisationId)

  await this.organisation
    .createQueryBuilder()
    .relation('coordinators')
    .of(organisation)
    .remove(userId)

  const org = await this.organisation.findOneOrFail({
    where: { id: organisationId },
    relations: ['coordinators']
  })

  return org.coordinators
}

This doesn't remove relation unless I change the queryBuilder to use organisationId instead of organisation entity.