The use case below is written assuming that you choose Altar as your faction, but I've run this through a number of combinations and believe it occurs regardless of which faction is chosen.

The opponents are listed in the following order (kingdoms on top, empires on the bottom):

Altar Yoren Capitar Tarth Gilden Parriden

Resoln Kraxis Magnar Umber Athos Yithril

The initial opponents are the leftmost two factions from the kingdom and empire lists, not including the player's chosen faction (e.g. for Altar, the opponents are Yoren, Capitar, Resoln, Kraxis; for Resoln, the opponents are Altar, Yoren, Kraxis, Magnar).

Add any opponent to the list, then remove any or all of the initial set of opponents (e.g. add Tarth, then remove everyone from the list except Tarth).  Click Back to return to the Choose Faction window, then click Next to return to the Choose Opponents screen.  All of the factions removed will be in the list again.

(A second issue: the list also sorts the factions, kingdoms first, then empires, so even if you do not do anything on the Choose Opponents screen -- e.g. immediately click Back to return to the Choose Faction screen, then Next to go back to the Choose Opponents screen -- the order of the opponents changes, since the initial list interleaves the opponents kingdom/empire/kingdom/empire.  So the first time on the screen, the order is Yoren, Resoln, Capitar, Kraxis, but the second time, the order is Yoren, Capitar, Resoln, Kraxis)

This is more of an issue if any of the initially selected opponents are removed from the list, and then the list is filled (e.g. remove Yoren from the list, then add all of the other factions):

Click Back to return to the Choose Faction screen, then Next to return to the Choose Opponents screen:

If you remove any of the factions from the list, the missing faction (due to sorting, this should always be Yithril) will appear at the end of the list.