First let me say that this is a great plugin. I just want to report what I think is a bug. A new version of Akismet came out about a day ago, and I promptly updated. But today WordFence is trying to tell me that some of my “Core” files have been modified. These files were all part of the Akismet plugin. They have not been modified from the current version of Akismet (the version I have installed).
So what I think is happening is this: since Akismet comes packaged with WordPress core, WordFence is checking Akismet’s files like core files against WordPress core. It should instead be treating them like the plugin files they really are and comparing them with the plugin repository.