It didn't trip me up so much as make me stop and go "...huh, that's odd," but I'll admit to having a related confusion with the same bits mouse_rr points out downthread.

It seems pretty clear that the A-plot of Arpeggio did not occur in UF; in particular, the "you are the first person of Earth descent to make contact with any ship of the Fog" line rules out the existence of Gunzō Chihaya during the original Fog War, and implies that Iona did not defect. Instead, it seems that Nagato and the other "Big Seven" just packed up and left for reasons unknown; they left some ships in place but without orders, and most of them, not being self-aware or -motivated, just went into sleep mode until the 'present day'. Léonne, Kongō, Maya, Iona, and a few others did develop Mental Models at the close of the Fog War, but seem to have retained the "no reason to do anything but follow my last orders" attitude anyway.

So, for me, this has three plot holes, and I'm not sure they are plot holes rather than To Be Explained Later-s, but here they are anyway: first, sans the Arpeggio A-plot it's not clear why the Fog developed Mental Models in the first place; second, given that some of them did, it's not clear why they retained the "no reason to do anything but follow my last orders" mentality after 400 years of experience (in Léonne's case, I suppose maybe it's that she was content to hang out on the beach in Hawaii indefinitely?) and third, those of them that didn't have Mental Models seem to have come up to speed on interpersonal interaction very, very quickly after being told about the concept. That last bugs me the least; maybe they can copy each other's notes, as it were.