current_page.children contains all subfolders, images etc and therefore they are displayed in contents layout and left sidebar in documentation layout. It need to be resolved propably by filtering the current_page.children in order_pages function.
Images can be solved by putting them in folder images on the same level.
As of now there is no version kept anywhere in the template files. Therefore users don't know which version their project use and if they should update.
Updating
So far I wasn't able to find any other way how to update the template in existing project other than initialize it again with middleman init MY_PROJECT_FOLDER -T hajnyon/middleman-uikit-documentation-template and then handle the possible overwrite of template files. If anyone knows about other way, please tell me.