I know there are thousands of threads for this question.
But I found out something really weird.
If you create a project on GitHub, do some commits.
Let\
I contacted Github staff from here : https://github.com/contact
Here's the answer (I couldn't do anything about it, no prune, no gc, etc)
Hey Maxime,
The commit was available because commits are not automatically deleted when they're removed from the history of a branch -- they're deleted when they're garbage collected. I just ran garbage collection for that repository manually and the commit should now return a 404.
Hope this helps.
Cheers, XXXXX
So you just have to wait or contact staff to force garbage collector in case you have the same problem !