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If you are failing to see your product categories while editing a product, but you can see the categories in your category edit menu, odds are your ‘children_count’ for categories isn’t correct on the database. A quick SQL statement fixes this: 
UPDATE catalog_category_entity SET children_count = "1" WHERE children_count < 1;


If you are still having problems, it’s also possible that your level is set incorrectly. In my case setting level to the root category for all categories worked great.


foreach ($categories as $category) {
        $category = $category->load($category->getId());
 
        $level = $category->getLevel();
 
        if($level > 2) {
            $category->setLevel(2);
            $category->save();
        }
 
    }