No, you should see four. I am assuming you are referring to the final boss fight. If I remember correctly I have seen the Shock Warden's appear close to or almost on top of the safe spots. And with all that is going on it is really hard to see the spots.
Sometimes symbol and that green outliner at the correct safe zone just dissappers, so you need to look closely, you'll see faint yellowish glow on that safe spot, indicates that this is the correct one. It's kinda hard too see but it is there.
Same thing can happens at the fight with Archivist, but everyone nuke him anyway, so it's not so noticeable.
Add: I'll try to make and add a screenshot when I get an opportunity.