I've not seen clips automatically being flagged as Rejected. Perhaps reset FCP preferences to see if that changes anything. Hold Option and Command while launching FCP and choose Delete Preferences. It will open the default Untitled library. Re-open the library you were working on, set the Settings back to the way you like them (disable background rendering, reset Import to Leave Files in Place, etc.) and see if the issue has been resolved.
After resetting prefs, make sure you go into Settings and disable background rendering. It's not needed except in certain situations, and even then manually rendering a difficult section is the better approach. Once you've turned off background rendering, you can likely recoup a lot disk space by deleting the cache. To delete the render cache, select the library in the browser, choose File->Delete Generated Library Files... Choose All Render files.
Manage render files in Final Cut Pro for Mac - Apple Support