Some feel they have found the fix to this issue. I haven't tried it myself yet, but I will when I get home today. Read the following:
"anakinxp1 wrote:
the main issue, check under your City Halls. You might find 15 or so decorative objects underneath.
If so, don't touch it.(it may crash

)
Remove few decorative parts to make some empty placement holds, then hit Alt ENTER to redraw the screen.
The objects under the city hall should be replaced(moved) to empty holders. Repeat till no more replacements of objects occur, for all your cities.
I assume this will free some occupied resources, and give you space for drops or spawns, and may saves you from resource overflow.
This means, you should claim dropped resources once in a while to keep safe margins.
Good space ex-spore-ation all!"
Also see the following link and check the incomming progress reports:
Zooming out of homeworld = Crash (kinda)