You just stated that you removed a Unique modifier. I don't claim to know anything about modding FF or civ4 for that matter, but that right there might be what is causing it. Is it possible that you might have accidentally removed the unique tag from Acheron or corrupted it in some manner? That is assuming it was your tinkering that caused it, which it may come off as I am insinuating this.
I have seen my fair share of, "where the hell did that come from" moments *(like for example killing the grigori, then them staying in the game causing anger in my newly conquered cities, and then trying to put another city in the game in barbarian world to get captured/killed again, which brought up the death text for Cassiel once again, but he still was stuck in the game)*, and I realize that you may have come across the perfect conditions in which Acheron could spawn multiple times.
Like Warkirby and the others said, try to replicate the bug. If you can find the exact conditions, it would be much easier to find out if it was some stray coding or something along those lines in either your or the FF teams, well, code.
Oh, speaking of bugs, I have one between the * marks, and I recall earlier in this thread that the Alter of the Luannitar (spelling, I know I'm terrible) victory wasn't working, which didn't turn out to be the case for me. Played a game as Banner, in fact the same one with the Cassiel bug, and had the victory via AotL. Speaking of which, the media for victories/the intro have been off for some time, but I suppose you know that
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Anywho, good luck in finding that bug out Omegon/FF team, seems rather strange.
PS: I have a 1781 exp captain in my stack o' doom. Was quite fun experimenting with nearly a full champion stack and not messing with siege units for a game. Also, the Banner module kicks ass
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