Maybe you don't have the current libs added to the fp-lib-table.
(you can test that by opening the footprint editor and trying to select the "missing" lib as your working lib. If it does not exist in this list, you don't have it in the table)
How to get all current libs from github into your fp-lib-table:
Open pcb_new or the footprint editor.
open the libary wizard:
preferences->footprint library wizard
In the window that opens select from github and make sure the text field contains: https://github.com/KiCad
If you always want the newest footprints deactivate save local copy.
(Otherwise this tool will download the current libs and add this local copy to the fp-lib-table. If you want that you need to first delete all old entries from the table. for that you can use the library manager in the preferences menu.)
select all (or only the libs you want, depends on your preferences.)
finish the dialog. (press next a few times until you can press finish.)
If the libs are in the fp-lib-table
Another option why you can not assign the footprints is if you use cvpcb and have some filter enabled.