There is nothing to fix. It isn't broken. Maybe it isn't as good as the best out there, but that doesn't mean that it is broken.
While I would agree in general, there is definitely (at least) one case where it is (occasionally) broken, being focusing with a wider angle focal length and aperture stopped down, from time to time yielding an image where absolutely nothing is in focus - even though focus was confirmed (and image taken with "focus priority" and "AF+MF" turned off).
Not being able to really tell from the small LCD screen just makes it worse, becoming aware of the issue only once you`re possibly far away from the scene (or the moment) already. Focus distance scale does clearly show the unexpected "jump" in case the focus actually failed, though, yet you need to pay close attention... at all times, eh.
Eventually, one just doesn`t have the confidence in the focusing system any more, being the worst, as you never know when it may fail (not to say lie to you), going unnoticed until it`s too late to retake (if possible at all, that is, even if you see it right away).
That said, I (still) do believe this can be handled with a firmware update, just that it takes a lot of time (years) already, so can`t really say when (and if) it will happen... Having the camera working fine in majority of cases is a clear indicator the problem is not deterministic (constant), so the "only" thing is to find out what throws the focusing system off in those certain occasions (can`t even say "cases", as none of the variables have changed, and focusing works for the most of the time in the same scenario already... except where it fails for seemingly no reason, and worse - lying to the user it worked fine).
Even just admitting it failed to focus would make the experience so much better already, regaining trust that once focus is otherwise confirmed the photo is actually in focus.