I have a similar problem I can't figure out how to get rid of, and it has completely ruined by campaign playthrough. I am on the third 'mission' and I have 2-3 of every hero I picked up in the first two maps (except my sovereign, only one of him). It has something to do with loading save games as that SEEMS to be when the hero gets duplicated, but I can't be sure since I don't always notice right away and I was only using quicksave/autosave so I couldn't go back more than 2 saves. I've noticed other very strange things happening as well, like I lose a battle, reload (yes I know I'm 'cheating'), fight the battle again and sometimes my sovereign is missing in the battle map, and then at the end of the battle theres a bunch of 'dead' units listed that weren't even in the battle. Also, my sovereign and champions sometimes get messed up during saving/loading. Most recent example is that I was playing through the third mission of the campaign, my sov hit level 12 and I put on this shiny new flaming sword I found, went through a dozen turns or so, reloaded an autosave, and my sov was exactly where he was the turn before but he had time jumped back to level 11 and my flaming sword was gone, replaced with the 2h life stealing sword he had been using previously. Its also worth noting that I had moved that sword to one of my champions when I equipped the flaming sword, so I checked, and sure enough that champion still had the sword, so I was now permanently missing my new flaming sword (it was a quest reward or something, which at my current point had already been completed so I couldn't do it again) and had two copies of the 2h life stealing sword.

At this point I got disgusted and quit. I was hoping at some point soon I could split these duplicate heroes out of my army and just leave them off in some corner of the map pretending they didnt exist (the first duplicates appeared in the first mission), but that doesn't seem like its going to happen until at least mission 4 and I've grown very tired of dealing with so many champions, duplicating champions, missing and duplicating items, etc.

This happened to me as well, although I wasn't sure on the exact steps to reproduce. Note to self, don't lose any champions in city assaults!

ive got the same issue. does anyone have a way to avoid this? i wont play again until it is. completely destroys any fun factor in the game. i can say for sure that no death or city attack is required to make this happen. also, all equipment from the duped hero is duplicated when equipped by another champion (1/2 the time, not sure why it dupes equipment, but the mage helm and cloak of shadows always dupes).

eventually, your stack is so large, that some are autokilled at the start of a battle. your sovreign is always the first to be sacrificed. 

worst of all, ive replayed the scenarios 3 times. its happened every time. having an 'epic' stack by chapter 4 is ridiculous, and with no way to remove the copies, it becomes a clicking game. click click click dupe some heroes every battle, etc. steamroll everything, but remove any character attachment you once had, because your originals are dead at the start of every battle. little help?

This is happening to me too. There are a dozen copies of one guy in particular that I keep killing. Pretty annoying.