Hello everyone and thanks for your replies !
I went to the ward office right after and they just asked me why I didn't registered earlier within the 14 days. I just told that I simply was not aware of this 14 days procedure and they wrote it on some "comments" section on paper. As well, they were kind of repeating the same thing 2 times like "oh... since August...well". But nothing very offensive.
After that they registered my resident card, and wrote my address behind it as the normal procedure is.
I don't know if it has any kind of importance, but I speak japanese. So it could help.
And that's it. I was not charged for anything. But take care, it's maybe because I did not exceeded another internal and non shared deadline (my case is less than 90 days but more than 14 days).
So to sum up:
- I just explained my situation and have been honest with it
- I was not charged for anything
- The procedure completed sucessfully and I got my resident record
If anyone come here for the same situation, I would advise:
Do it right away and be honest with your situation. If possible speak japanese to simplify the communication.