On the contrary, I was able to pass through everything without any problems. Because of this, I even replayed the mission from the beginning, as there were still unvisited upgrade locations left. And as it turned out, I couldn't go back.

Crazy_Mary, try to complete all the secondary quests. Maybe they aren't so secondary after all? Nothing else comes to mind.

Yes, I remembered something else. Some of the prophets didn't teleport me immediately. I had to enter them twice.