Do not ever launch the base game, after GA is installed.
That is possibly what caused this issue - it confuses the database because it doesn't know how to deal with the expansion content, when you launch without the expansion. So it attempts to fix itself (you would probably see Updating Content Database when you open the game), but usually doesn't do it properly and so it causes various issues.
I would recommend you share all creations (if you have any unshared), and then fully reset your game. That would be the easiest option, but will remove saved games* and all downloaded creations.
To reset your game, just delete (or move/rename) the entire Spore folder located at C:\Users\your_name\AppData\Roaming
*If you move/rename the folder, instead of deleting, you may be able to recover saved games... but it is not guaranteed to work. If you do want to try and recover them, keep the Spore folder in a safe location, and let me know, I'll give you more detailed instructions for that.
However, just in case there is an issue with C&C, I would also recommend you fully reinstall as well, after removing the Spore folder.
Uninstall the base game and both expansions, and reinstall Spore > C&C > GA from Origin. Do not launch the game until after everything is fully installed (and only launch GA, never the base game).