Thanks guys, yes I do understand bugs happen and I would not fret (much) about stats that I personally don't even use for anything important.
What I am greatly concerned about is the fact that Google employees make important decisions about my sites, such as whether to ban them all together as they did in 2011, without actually looking at the sites and flying completely on instruments, as far as I can tell. I don't know if this is not to reveal what exactly they check on my sites or simply for expediency, but the actual Google-badged (or contracted) humans do not visit the site in order to respond to a reconsideration request.
They appear to be using only the backend data and if WMT data is any indication of the quality of the data they have about my sites, I think I should be worried. In this particular example, I don't think for a second that anyone [human] at Google will make an effort to see the source of the pages they think have links to my other sites. "The backend says they're interlinked, then they're interlinked! Here, let me pick the right penalty for you!"
Anyway, this is a bizarre situation in which there's no recourse because there's really nothing I can "fix" as such because nothing is broken. I was (still am) considering sending a reconsideration report but I'm afraid all it's going to accomplish is to draw attention to the batch of bad data and nobody will take time to look at what's going on, they'll just trust the data.