Yes, each region has a base culture. It's determined in the "SetAttributes::" section for each region. When you place troops which are not of the same culture, it's a good idea to put an extra bit in the "MakeUnit::" line for that region forcing the culture. You can see how it's done by looking at the early.txt file and examining the MakeUnit:: line for Naples. See how it adds Orthodox_Culture after the unit size and then has the //remark about forcing a Byzantine unit?

I don't really see how adding Aragonese, who are Catholic, to Flanders or Champagne, which are both Catholic, would cause this error. Are you sure you didn't make some changes to units elsewhere? Adding an orthodox only unit to a catholic region or a catholic unit to an orthodox region? If you didn't, it still might be worth trying a fix by just adding the Catholic_Culture right after the unit sizes for each of the starting units in the regions you've changed.

I hope that helps. Good luck!