Yeah I definitely had something like this happen. I went Worldbreaker first instead of Oneiros and by the time I eventually did a single Oneiros fight I’d already fought him twice.
Old issue that never got fixed, see [REPORTED] Incorrect opponent teams in world events. Whenever the battle map repopulates the battle icon shown may still contain the team composition of the team that got replaced. Restarting the game updates the team composition to the correct troops.