Correlation is too strong a word, but I have a suspicion
Statistically speaking, you're right -- it is too strong of a word because I haven't made any direct calculations and have only looked at a handful of sites; however, I have a hunch based on some of the sites I've seen, even my own.
I did find some of my own articles were linking back to the homepage using my phrases contextually, sending visitors in circles. It does seem that if the homepage is optimized for a set of phrases (via title, img alt, header tags, AND internal pages link back to the homepage with those terms, it could really be over the top. I've corrected those, and I only found 4 instances sitewide, but it may have been enough to trip the filter.
I am still digging, so I will post an update if I find something more definitive, or see any improvements as a result of my changes.