I just got to lvl 40 and my file is smaller than 10 mb, but I'm beginning see a lot of stuff going "wrong".

It's not that game breaking, but can be annoying, like Serana asking every minute "Yes, what do you need?", and other strange things like my character always grabbing the glowing burning end in the forge animations. There's also a bard at Solitude with a torch permanently glitched into his hand, he even goes to sleep with it.

I already play the janitor style and auto-saves off.

The only there that I have is Viarmo holding that damn torch all the time.

All that is normal. The Serana thing stops after you complete the castle quest. Advice if I may: Don't play the Skyrim cleaner. It's boring and it doesn't do anything.