Is it only WordFence that shows the needed update, or does it also show on the WP admin bar?
WordFence creates a bunch of db tables. Have you looked in some of them for this? Maybe you could search for critical severity?
Worst case, if you can't find it, I think you could tell WF to ignore this issue?
Any chance this is a subsite in a multisite install? I have several sites in two different multisite installs that always show phantom updates needed-- in the admin bar, not WF-- and I haven't been able to find where that is coming from!