Hi Filippos,
You said "
I set the article ID's to display and I have a menu item for them".
But it seems that you do not have a Menu Item for those articles.
I know that you think you have, but it really seems that you don't.
Not having a Menu Item of type "Category Blog" or "Single Article" is the only possible reason why you have your URLs like
/component/content/article/19-category/68-emak?Itemid=101.
Just create a Menu Item of type "Category Blog" for the category of the problematic articles and the issue will be gone.
For more details, please have a look at
this discussion and make sure that you watch the video that I recorded there (watch it in Fullscreen and FullHD for better quality). It shows everything in great details.
Our particles have nothing to do with the routing.
The routing and the URLs are determined by the CMS (Joomla) and the way you have configured it.