I looked around and didn't see this reported yet, so here's the issue I ran into. Conversation started with the animancers, and conversation ended with me accepting Aloth into the party, however, he did not join the party, the UI window to change my party comp did not pop up. Now he's just standing here like any other NPC, and when I click on him he says "Let us speak again once we've left Port Maje." I have no conversation options to add him to my party whatsoever.

Hm, that's strange. I've never noticed that before. If all fails then he should move to Port Maje if you finish the main quest there and get your boat.

Update: I continued the campaign and got to my boat. Aloth was not there. I went back to the dig site and was able to have a conversation with him but could not get him to join the party. Same thing happened to Serafen.

I am dealing with the same thing right now, did you ever find a solution?