When a user makes changes to the default global menu layout they are stored in "~/.config/menus/lxde-pi-applications.menu", so each user can have a personalized menu. It's likely that you have accumulated some duplicate entries, or the file has gotten tangled up for some reason.
Let's save the file you have now (by renaming it), in case we need to replace it. Probably not, but it's a good habit to always make a backup of a config file you're going to edit or delete. In this case we want to delete the file and save a copy, so we'll just rename it.
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cd ~/.config/menus
mv lxde-pi-applications.menu lxde-pi-applications.menu.broken
lxpanelctl restart
Doing this will reset everything to the original default layout, as you no longer have a "lxde-pi-applications.menu" file.
Now use the menu editor and it should work correctly, creating a new "lxde-pi-applications.menu" and adding to it as you make changes. This will of course wipe out any previous changes you've made to the layout, but new menu items added by you or a program install will still be there, just maybe not in the same location in the menu.