Nest spawning is broken...maybe it's a modification that affects the creature's stage or the generation of the planet's terrain.
In any case, after removing the modification that changed the landscape and nest spawning in such a way, you will need to clear the cache of the game "...AppData\Roaming\Spore" by deleting the files: GraphicsCache.001, GraphicsCache.002, GraphicsCache, Planets, Pollination...
N.B. By the way, if you want, you can try my modification. I went from cell to cosmic stage testing it. It seems that I did not find any glitches (except for the old ones from the Spore itself
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