Okay, this just happened to me again. This time the number of cities in the world went from 8 to my 5 (another change of 3 cities) and the number of units in the world went unchanged at 128. One thing in common between the last game and this game is this debug message on the second to last turn:
Debug Message: WARNING: Unit Troll is owned by a player but has no sovereign, , so it gets no experience.
Could be another coincidence.
Full debug.err:
http://pastebin.com/WQU6DhEf