If you've installed a gamecube game to your SD card, it should be located in sd:/games. If you don't want it anymore, it's safe to delete. If WiiFlow tried installing it like a Wii game instead, it would be located in sd:/wbfs (and wouldn't be playable anyway).
If CFG is trying to install things to SD instead of USB, you may want to check your default settings, or better yet, delete your settings config file and force it to build a new one the next time you launch CFG. Be sure you're running a recent version (at least v70r51, if not the latest). If you are still running v70, you're running an old version and should update.