Something is wrong with documentation or me. I do all what documentation says.
When i put in terminal :
$ php vendor/bin/doctrine orm:schema-tool:c
I had the same problem when creating a new doctrine config in a new ZF2 module.
problem was caused by
'User\Entity' => 'property_entities'
the user part was from the old entity
'Property\Entity' => 'property_entities'
Changing that fixed the issue