Hi rasoulezzat,
There may be some confusion caused by my using the term TOC in several different ways.
You can create a TOC page. On that page you can put wiki links or any other text or content you want. You would not use the TOC shortcode in that page.
This page has a screenshot of my TOC page and some discussion about it:
https://www.davidmccan.com/wiki/special-toc-page/
The TOC shortcode is useful for using in the sidebar and for using in other wiki pages to have a table of contents. You could create a page and put the TOC shortcode in it, but not name it TOC.
On this page, for example, you can see the TOC shortcode embedded in a two column page on the left, and in the sidebar on the right using the Yada Wiki widget:
https://www.davidmccan.com/wiki/plugin-overview/
On the Frequently Asked Questions page of the wiki, the FAQs are a wiki category and the list was created using the TOC shortcode with the category “FAQs”:
[yadawikitoc show_toc="true" category="FAQs" order=""]
You should not have to create categories in the posts section. I just tried on my test site (localhost/wikitest) creating a wiki category and a posts category with the same name ‘desserts’ and they did not get mixed up. The wiki category page was:
https://localhost/wikitest/wiki_cats/desserts/
It only showed the wiki article in its list. The post category page was:
https://localhost/wikitest/category/desserts/
It only showed the post category item.
In your admin area, under settings/permalinks, do you have ‘Post name’ as the setting?
I hope something from my rambling above is helpful or gives a clue for you. If not, please let me know and we can investigate more.
Best regards