Any chance you're on Win10? I am, and I've experieced it too. That might cause it. Win10 (Creator Update to be specific) fucked up the calibration for some older games including SPORE. If you Alt-Tab out and then back into the game this glitch will happen.
The only workaround is to never Alt-Tab when playing SPORE, but if you do, then press Alt+Enter twice to exit and instantly re-enter Fullscreen. Then it will work as intended until you Alt-Tab again.
In my humble opinion, the only stage that is genuinely difficult on Hard is the Civilization Stage. You just HAVE to use exploits like the 100% Speed/100% Power Vehicle switching to succeed.