Atommannj,
I encountered the same problem under 1.01, and had to start a new game. However, since upgrading to 1.02, it has disappeared, so I believe Brad has fixed it. You may want to restart and see if that solves things.
The only CTD I am now encountering, is when I eliminate an AI empire and attempt to access its diplomacy or stats screens (to verify that I have taken all its planets or reduced its economy to zero). Should I wait a turn, though, the program will correctly calculate that the position has lost everything and remove any maintenance-requiring ships, SB's, etc., allowing me to continue play.
~SDC~