I used to think they would happen sometimes when I "changed the gamemode" (EG. playing a campaign then starting an expedition (vice versa works too), or safari, or even just switching slugcat).
I then discovered with Artificer (the dream sequences would sometimes do that) that while we're stuck in one, my controller would vibrate, indicating the end of a cycle approaching, meaning that the world was running but no input seemed to do anything (the only exception being when you disconnect the gamepad, the pause menu would pull up and sometimes let us abandon the cycle normally).
(if you did that before 30~ish seconds, you wouldn't loose karma like "expected")
However, today, it happened without me even switching modes, precisely with SpearMaster, but I also used a passage (The Nomad from Outskirts SU_S03 to Shaded Citadel SH_S02) to get that bug.
A graphical glitch appeared too (see screenshot), and once the loading was abnormally long enough, I quit and I now confirm I haven't lost karma.