Woman largely can't join the culture of a friendly wave while passing and have to simply not engage in any interaction with any man. I feel this every time I have to decide; do I wave in passing, and if I do when I'm then blanked. This shows that the men who do this are also runners.
Calling it out isn't enough. I nearly never see it happen, even though it happens enough to be a real problem for women. We have to proactively change this culture in our running circles, part of the problem is hiding in this group. Cat calling is never ok, you wouldn't do it to a male stranger. But also examine your motives if you wave or say hi, are you doing it for the same reason you do when you see another man or are you imagining more?