Duplicate units are eithor in parrallel or in series. In parrallel there will be 2 of copies of the unit placeable in the editor which might happen only if they are given different identifiers but have the same physical name. Two units with the same identifiers will be put in series, based on the order of the mods they originate from in dependiencies (if you edit them for the map the changes will always be applied last).
Basically, all the campaign units are in series, often with their melee counterparts. Editing their data will add yet another layer which is your changes to them however when the map loads it all compiles down to 1 unit with the last applied mod's stats (your map's if you altered them in the data editor).
Consider checking if it is at all possible to remove some of the mods to reduce duplication.