I encountered a similar issue recently, but with auth permissions.

It is described here: https://code.djangoproject.com/ticket/29843

On Wednesday, October 3, 2018 at 1:01:37 PM UTC+2, Marcin Nowak wrote:
>
> Hello.
>
> There is a huge issue with content types framework. The data is loaded 
> after every migration (post_migrate signal) automatically, and this 
> approach is against db data consistency.
> The biggest problem is with data migrations, which are applied at the 
> first time (on clean database). Any data migration which depends on some 
> content types will not insert the data.
>
> The sequence looks like this:
>
>    1. create db
>    2. insert into auth_permission ...  inner join django_content_type ...
>    3. post migrate: insert into django_content_type ...
>
>
> Two things are wrong:
>
>    - automatic creation of content types
>    - creation of content types after running migrations
>
> Solution:
>
>    - creation of new app should add very first migration, which will add 
>    entry to the content types
>    - create_contentypes handler should be removed from post_migrate signal
>
> Any data migration, which depends on some content types, should be 
> declared with proper dependency. This will guarantee existence of the 
> required content type entry.
>
>
> BR,
> Marcin
>
>
>

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