When we switched to using a tiling window manager for all our windows, we ran into a muscle memory problem. We were used to jumping between emacs windows/buffers using C-x o and C-x b and then without thinking about it we'd try and use the same keys to jump between i3/sway windows and of course it doesn't work. Or vice versa, trying to use i3/sway shortcuts to switch emacs windows/buffers.
To try and solve this problem I've been using less emacs windows and more i3/sway windows, so I can just use i3/sway keybindings everywhere, but emacs puts up some resistance to that. I like this approach