I got multiple errors related to it. I mean it is possible to open more than 39 slots for civs. Also it is possible to add repeating civs and leaders If you MUST use worldbuilder then save map as scenario and do cleanup of that scenario. Most important thing was existence of civ with all techs. So if it wasn't your fault, then somehow civ spawning glitched and spawned civ with all techs. Upload your scenario, User Settings and BTS INI file (its here C:\Users\<USERAME>\Documents\My Games\Beyond the Sword). Adding some techs could have break game too. Use custom scenarios or generate map and stay away from WorldBuilder as its VERY easy to break game.