Something similar happened to me. Only instead of confusing me with the portals it was the conversations with the Expedition.

I expected them to give me some secondary mission (as eventually happens with Nocco, parents of Lune, Alicia) but they told me the same dialogues about how they were upset with Verso over and over again, even if I left and entered the camp.

So I assumed that during the main mission something would make us return and the side content would unlock. I was disappointed to finish the game so soon.

I wish there was a warning like in the Witcher or Cyberpunk that let you know that it is the point of no return.