That was my experience also especially the past year. I do programming and design and it seems many apps twist the ui api to do things that you can't naturally do in the interface and so Yabai, completely oblivious to it, will try to manage it and you have elements disappearing or appearing too large/small, behind other elements, etc. Even if you create exceptions, it seems things sometimes slip through the crack or start behaving unexpectedly. Flipping between native tabs for instance start throwing the tiling off for some apps that I use.

Yabai used to be pretty solid and usable, but I think with the author not using a Mac for his daily and with all the updates to the OS that he has to keep track of (and how some windowing Mac api are still blackboxed or not reliant to build logic atop of) it's only a matter of time before it gets into a poorer state.