When I was doing the objective in Chapter 2 and Chapter 3, that required it, the only ones that seemed to count were the Chaos Rifts that had actual rifts spawn in them, which not all the Chaos Rifts do… they aren’t very common (at least, they aren’t for me). I don’t know if this is intended or not.
Looking closer at this…
In the Chapter 2 objective “Chaos Rises” and the Chapter 3 objective “Infiltrated Dreams”…
One of the requirements uses icons rather than words. They state we need to locate Chaos Rift events (represented by the Chaos Rift icon) and then close rifts (represented by a rift icon, which is the same icon that appears on the map when an actual rift appears during one of these Chaos Rift events).
So, it looks like what was counting for me to allow me to complete those specific things are probably intended. We need to close actual rifts that spawn from the Chaos Rift events.