Cool!
As I said, I suspect something you did that was not updated (as you may expected) on the PCB.
but for me it sounds as expected.
There is one important concept on KiCad different from (as I learned) EDA tools software products:
On KiCad there is no fixed (locked) association between symbols, footprints or 3D files.
It is possible however to assign a footprint on a symbol, so when you use on schematic you can add that symbol and then you dont need to associate the footprint.
It may be the case that you were expecting that when you change something on schematic that will match immediately the footprint changes on PCB. Depending on your library that you are using (the symbol) and how you did the update (import of the netlist) it needs to have a more understanding on this step.(choosing the right options for updating or not the footprints)
- this is not a limitation of KiCad but a flexibility on its choises to the workflow.