The NES Mini:
Only installed 715 NES Games
No other console games
You can have one of several issues. 1. Using bad rom sets. 2. Having improper folder management. 3. Improper Command Lines, and so on...
I would suggest you uninstall ALL HMODS, and use the ones in my set that I compiled, put together, revised, and so on...
https://www.reddit.com/r/nesclassicmods/comments/6j2zoo/the_mega_hmod_thread/
First try this. As you add the games, (making sure you install Standard RetroArch from my Set, which has both updated Nestopia & FCEUMM), at the end of each command line, leave a space, then put in one of the following arguments...
--retroarch --fceumm
OR
--retroarch --core nestopia
Either of these commands will ensure you are using Nestopia or FCEUMM instead of the default NESC Emulator, which has a lot of issues with many mappers.
If you still have issues, then, you likely have Good-Set NES roms, with md5 hash checksums that just aren't optimal for the NES Classic Environment. You will want to switch over to using No-Intro Set. Keep in mind, don't take these names literally. They are just release groups! Good-Sets are amazing. They just don't work quite as well on the NES Classic, as they do on other Set-ups!
Lastly, use Folder Management, and I would recommend 30 Games per folder, to guarantee 4 save states per game. Once you bypass 30 per folder, you start losing save states.
I have never had an issue with saving NES Games, as I have always followed the above criteria, as far as my set-ups.
You can see a general set-up I use, at 2500 Games, and still with no C2, C5, C6, C7, nor C8 Errors, because I addressed the Memory Limitations as well as I could, considering. C6, for the record, is a read error, similar to a CD Skipping. So, one of the things I mentioned, should take care of your issue.
My 2500 Game Build