The fourth portal happens to be in precisely the same place as one of the portals in the parallel universe.

However these portals work, the connection between them exists on a different plane. Unbeknownst to anyone in either universe, that plane is shared by both universes. The portal projects in both universes have been punching holes into a shared dimension, and so it was only a matter of time before the two collided.

If only one universe was doing portal stuff, they could build as many portals as they want with no problem.

By pure coincidence, our fourth portal was built in precisely the same position as one of the portals in the other universe, and so now the portal systems are linked.

Perhaps it's even possible that the two networks could be disconnected if either of the two overlapping portals were destroyed.