This only happens on the first playthrough of a new area. When entering the Barren Aqueducts, for example, the entrance to the area is right next to a portal. As such, it doesn’t play the animations and light up. Visiting the area later or using the portal to arrive to the area correctly shows that the portal is lit up.
This particular example happened in The Felled Wood on my way to the Soulfire Bastion.