I think I know what happened to you. The destruction of the bases coincided with the AI "siege" mode. In this mode, the AI spends some of its "action points" on creating new bases near the player. Destroying the base gives these "points", and much more than the natural increase.
However, I was going to change this in the next releases, since the player cannot know which mode the AI is currently in. Also, it is planned to weaken the expansion in general, since after the bugfix in 2.02.00, it became too effective. The exact release date is not yet known.
I downloaded the saves, they will help me