There is another barrier across the channel south of the harbour, in the Red Hammer tribe area. At least in D2:ED there were 4 goblin ballistas with a blue lightning effect around them that you needed to destroy; one was just inside the barrier, but could be taken out with Dragon Burst or maybe Dragon Breath (Fire Spheres were blocked by the barrier).
The goblin village barriers aren't there in DKS. Once you handle the initial one in the cliff base, you're free to fly all the way to Kali's fortress.
It sounds like the problem here is the game isn't detecting that you're leaving the area, thus triggering the transition to Kali's fortress. I don't know what a fix would be though, besides trying again. Warp back to your tower and fly all the way back and see if it works. If it doesn't, contact tech support.