Apparently the problem is alacarte. I can get the new profile to have the leftover file if I touch the menu item in alacarte (i.e. unheck and check it). I'll file a bug for that, I guess.
In any case, it would still make sense for the package to remove the file in ~/.local/share/applications. Not sure if this affects other packages.
That's not a bug in usb-creator. The package manager certainly shouldn't be removing files that it doesn't own, from users home directories. I'm not really sure of any way around this, but I'll keep the bug open for now.
That's likely due to a left-over desktop file in your profile. Could you please try with a new user profile and see if that exhibits the same issue?
Thanks