Magento 2: Problematic Category ID? “No such entity with id = 0”

Ive come across a problem im not able to handle by my self. I have recently started the process of moving my M1 store over to M2. All in all, a solution like Store Manager from eMagicone makes the task pretty smooth, but some issues are there. I have some problem i do not understand with categories. One of the custom extensions im using allows customers to browse through all products but it seems to be something wrong with category entities and throws this error: a:4:{i:0;s:26:"No such entity with id = 0";i:1;s:16195:"#0 /home/admin/domains/test/public_html/test/app/code/Magento/Catalog/Model/[login to view URL](141): Magento\Framework\Exception\NoSuchEntityException::singleField('id', '0') There is also an issue when trying to edit a product, the correct category path is not shown, it only shows root category ID 2, while the product is assigned to a store that is using root category ID 3. If i disable all custom extensions and only have Magento alone, the error still is there when editing products. I have trying to add in catalog_category_entity a field with entity_id 0, since it started from 1. No difference, exact same error message is shown. This is clearly some error in DB, could any one help me with some suggestions? Magento 2.1.2 - Php 7.0.X, MariaDB 10.0.X Other than on that specific page for that custom module, there is no issues on frontend that can be linked to the same. When browsing through layered navigation, all categories shows up where they should.. One stack trace related to the problem is attached