Consider this: I have a repository on, for example, GitHub, and add a file I wrote.
I forget to mention the file in the license, and publish the updated version to the repository, realizing the mistake after it is too late.
So I fix the license and publish it shortly after.
Now, the old version of the repository is of course still visible, with a file not covered by any license.
Can this be exploited? If so, what can I do to protect the repository?
Files not covered by any license notice are considered "all rights reserved". I don't see how this can reasonably be exploited in any meaningful way.
If you like, you can with many source repositories rewrite the history even after it happened and for example merge multiple commits.
A license grants others the right to copy and use your code under certain terms. Without a license, others have no right to use your code. This question expands on this. Unless you specifically relinquish your rights or allow others the right to use it, you are the only one that can use it.
You are the only one that can exploit that situation, if you haven't granted a licensed to anyone to use your code, you have the right to chase copyright infringement.
But realistically, based on the history of the repo, you could have trouble enforcing the use of one file that was unlicensed for a short time. It is easy to argue that you released the code under the same license that is globally advertised for the repo, having part of the code unlicensed for a short time could be attacked as deliberate entrapment.
