in kali applications menu, there is '01-01-dns-analysis' menu but in gnome-shell menu 'information' category does not contain '01-01-dns-analysis' which causes dnsenum and some other tools to appear outside of 'information' category in gnome-shell 'show all applications'. to fix this use dconf editor and navigate to
[org/gnome/desktop/app-folders/folders/info] and add '01-01-dns-analysis' to 'categories'.

in kali applications menu, there is '05-01-online-attacks' menu but in gnome-shell menu 'password' category does not contain '05-01-online-attacks' which causes hydra and some other tools to appear outside of 'password' category in gnome-shell 'show all applications'. to fix this use dconf editor and navigate to
[org/gnome/desktop/app-folders/folders/passwd] and fix '01-online-attacks' to '05-01-online-attacks' in 'categories'. this looks like a typo.

ace, arduino, baksmali, smali does not have a category to be included and therefore they are not displayed in kali applications menu and only in gnome-shell 'show all applications' outside of kali categories. a new category must be created and the desktop files for these tools should be edited in order to include these tools into the new category.