The footprints you use in a design are not updated automatically. They are copied into the header of the pcb_new file. You need to trigger the update of footprints in a design or add new footprints to it to get new files from github.
But if you make a new design, new footprints are used which means that it can happen that a footprint you successfully used in one design suddenly has problems in a new design.
This is why it might be a good idea to use the kicad libs only as a starting point for you personal verified library.
Kicad does not really use git. It uses the github api do download a zip archive. Don’t ask why. (I think @SchrodingersGat mentioned that someone in the development team is quite attached to the github plugin. A real git plugin would be nice.)