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I was able to reproduce this issue when installing sample data are installed after the module.
The reason is that some category are created with the is_anchor attribute set to false.
It is impossible to have this with ElasticSuite.
A quick patch is to update the is_anchor attribute into the database:
UPDATE catalog_category_entity_int SET value = 1 WHERE attribute_id IN (SELECT attribute_id FROM eav_attribute WHERE attribute_code LIKE '%is_anchor%');
If you have custom code (mostly import for categories), check the is_anchor attribute is set to 1.
This issue seems to occurs on multiple websites instance.
Symptoms :
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