Now I believe, this is a bug in package "kali-menu". I tested several things. First, I created a fresh user = same issue. Then purged kali-menu and it`s dependencies and as expected, all whisker entrieds where gone.

After this reinstalled only kali-menu = kali entries appeared again, same issue.

To make sure, needed libs and so are installed, I reinstalled kali-desktop-xfce = same issue. Then reinstalled kali-desktop-lxde and kali-deskto-kde, as they where deinstalled by deinstalling kali-menu (dependencies).

To make sure, that kali-menu or whisker will not read double entries, I deleted entries of double shown applications. First try, move entry in /usr/share/kali-menu/applications away, then moved back and moved the same
entry away in /usr/share/applications/. Both tries got no changes, the issue stayed.

Wha, do I believe, this might be an issue in the package? Well, I am running another computer with same configuration (XFCE4 and whisker plugin). Although this computer was only upgraded (no manual configuration done by me ever), the same issue is showing there, too.

Please note, that the double entries are only shown in whisker-menu, but NOT in standard XFCE application menu. I checked with KDE, LXDE and XFCE (as said, standard menu).

Of course, might be also a problem with the package "xfce4-whiskermenu-plugin", but I can not prove it.

Hope, this helps a little bit.

Best regards

Hans

The double entries appear, when you have set either "listview" or "icon view" in the settings of whsikermenu. They do not appear, if you set "tree view", which is preconfigured in kali.
Maybe because this, this issue was not discovered before?