It should be much easier to fix Waiting for Other Civilizations now after the WorldBuilder 3.9 merge.
Open C:\Users\[your user name here]\Documents\My Games\Beyond the Sword\Logs\BBAI.log
(If you forgot to turn on logging, I think it may now be possible for you to save the game, turn logging on, load the game, and then find what you need in logs even if it won't have much info from before the problem.)
Find the Unit ID of the last unit mentioned in this file, and the player who controls it.
Open World Builder.
Select the player leader head icon to open the Player Data screen.
Using the drop down menu at the top left of the screen (below the Kill/Revive Player and Switch Player buttons), switch to the player whose turn it is, whose unit is causing problems.
Use the drop down menu at the bottom left of the screen to switch to the "Units + Cities" screen.
Find the problem unit (which is easier if you first reorganize the unit list by unit ID, by checking the Unit Id section header) and select it. This will take you to the Unit Data screen.
Press the Kill button.
Close the Unit Data Screen.
Close Worldbuilder.
The WoC issue should then be solved, at least for a little while.
It is possible that the AI is having trouble deciding what to do with multiple units, requiring you to use the same method to kill more then one of them.
It is also possible for there to be a WoC issue caused by something other than a unit, but that seems to be pretty rare.