Content entity type ids are being gathered in the wrong way in the dynamic_entity_reference_field_views_data(). In my case, some entity types that were created using the ECK module didn't have a translation of their entity type label. They were not included in the list. The relationship plugin wasn't defined for them in a case the current site language is not the default language (English). The relationship plugin was "broken" and JOIN wasn't added to the view query.
The patch will be added below.
Closed: won't fix
1.0
Code
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It's likely this issue predates Contrib.social: some issue and comment data are missing.
This sounds like a won't fix to me as this issue will also be present for ER field in core .It should either be fixed in ECK or core.
As a workaround, if ECK doesn't support 'entity type label' then please implement hook_entity_type_alter and set it up.