New to bspwm since yesterday and a question for the bspwm-masters:
It’s not technically two different firefox instances, it happens when something pops up in a different window in bspwm. Closing the popup will close both the popup and parent window.
the exact lines to close a window in my .sxhkdrc are:
super + shift + q
bspc node -{c,k}
so i think maybe that is the problem as it says c for close an k for kill?
Doesn’t look like the default entry 
Also it’s technically wrong syntax. There are no options in keybinding, but there is an option in command (c and k). Since there isn’t an option on keybinding, the k flag is executed everytime.
Here’s the relevant line from bspwm edition - which is also a part of the default config.
Here, super+w will close window (the behaviour you need). Super+shift+w will kill all instances (the behaviour you’re experiencing)
my mistake, as said i am a novice with bspwm.
super+q does indeed close the selected window, while super+shift+q closes all instances.