Proszę poradzić co jest nie tak. DoctrineMigrationBundle wygenerował zapytanie które zwraca błędy INTEGRITY CONSTRAINT. Poniżej wklejam wyniki komendy i eksport istniejącej (kłopotliwej) tabeli

doctrine:migration:diff (fragment)

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    public function up(Schema $schema)
    {
        $this->addSql('CREATE UNIQUE INDEX UNIQ_DFCCB96DEDE56D28 ON shop_division_position_link (division_position_link_did)');
 
    }
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doctrine:migration:migrate

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Migrating [32mup[39m to [33m20180310185535[39m from [33m0[39m
 
  [32m++[39m migrating [33m20180310184729[39m
 
     [33m->[39m CREATE UNIQUE INDEX UNIQ_DFCCB96DEDE56D28 ON shop_division_position_link (division_position_link_did)
[37;41mMigration 20180310184729 failed during Execution. Error An exception occurred while executing 'CREATE UNIQUE INDEX UNIQ_DFCCB96DEDE56D28 ON shop_division_position_link (division_position_link_did)':
 
SQLSTATE[23000]: Integrity constraint violation: 1062 Duplicate entry '17' for key 'UNIQ_DFCCB96DEDE56D28'[39;49m
 
[37;41m                                                                                                                                                   [39;49m
[37;41m  [Doctrine\DBAL\Exception\UniqueConstraintViolationException]                                                                                     [39;49m
[37;41m  An exception occurred while executing 'CREATE UNIQUE INDEX UNIQ_DFCCB96DEDE56D28 ON shop_division_position_link (division_position_link_did)':  [39;49m
[37;41m                                                                                                                                                   [39;49m
[37;41m  SQLSTATE[23000]: Integrity constraint violation: 1062 Duplicate entry '17' for key 'UNIQ_DFCCB96DEDE56D28'                                       [39;49m
[37;41m                                                                                                                                                   [39;49m
 
[37;41m                                                                                                              [39;49m
[37;41m  [Doctrine\DBAL\Driver\PDOException]                                                                         [39;49m
[37;41m  SQLSTATE[23000]: Integrity constraint violation: 1062 Duplicate entry '17' for key 'UNIQ_DFCCB96DEDE56D28'  [39;49m
[37;41m                                                                                                              [39;49m
 
[37;41m                                                                                                              [39;49m
[37;41m  [PDOException]                                                                                              [39;49m
[37;41m  SQLSTATE[23000]: Integrity constraint violation: 1062 Duplicate entry '17' for key 'UNIQ_DFCCB96DEDE56D28'  [39;49m
[37;41m                                                                                                              [39;49m
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export sql istniejącej bazy (tylko tabela kłopotliwa)

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CREATE TABLE `shop_division_position_link` (
  `division_position_link_pid` int(10) UNSIGNED NOT NULL,
  `division_position_link_did` int(10) UNSIGNED NOT NULL,
  `id` int(11) NOT NULL
) ENGINE=InnoDB DEFAULT CHARSET=latin1;
 
ALTER TABLE `shop_division_position_link`
  ADD PRIMARY KEY (`id`),
  ADD UNIQUE KEY `UNIQ_DFCCB96DF6CA6684` (`division_position_link_pid`);
 
ALTER TABLE `shop_division_position_link`
  MODIFY `id` int(11) NOT NULL AUTO_INCREMENT, AUTO_INCREMENT=5;
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Przecież masz wyjaśniony błąd.

Masz zduplikowany wiersz z ID = 17 w tabeli a próbujesz nakładać UNIQUE.

Więc masz problem z danymi a nie z wygenerowanym zapytaniem.