I ran into the same problems, my guess is that it has to do with a maximum of units for custom battles. The solution might be to use the mp edu from your install folder\eb, which has less units for each faction, or to remove the ownership for certain regional units, or to paste the unit info higher up in EDU.
I am somewhat guessing, though I think it worked for one of my ctd_placeholders that I used to track ctds.
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