diffDatabaseToChangeLog / updateDatabase tries to update table in Reference database

When creating a sql file to update a database with an older version I am having problems with Foreign Keys. I expect liquibase to correct any errors / problems / differences in the database I specify, but it keeps adding entries to update my Reference database:

ALTER TABLE `reference_db`.`table` ADD CONSTRAINT `FK_ght3cbd158a0kf1fq19b6mlml` FOREIGN KEY (`id`) REFERENCES `reference_db`.`base` (`id`) ON UPDATE NO ACTION ON DELETE NO ACTION;

ALTER TABLE `reference_db`.`table` ADD CONSTRAINT `FK_s4xwdnbr0x3ga73ljhxb2jllm` FOREIGN KEY (`parent_id`) REFERENCES `reference_db`.`base` (`id`) ON UPDATE NO ACTION ON DELETE NO ACTION;

Instead of these entries I would expect that the keys in the database I try to update are adapted to be the same like in the reference database (which is built from scratch only to make the comparison).

I tried updating to liquibase 3.1.1, but besides other problems (https://liquibase.jira.com/browse/CORE-1900#icft=CORE-1900) that make it unusable for the time being, the problem persists in the latest version.