I think the biggest risk though is acutely doing high intensity exercise (e.g. a marathon) whereas doing low intensity regular exercise (e.g. a 5k jogged at moderate pace 4x a week) is probably good.
So it's not "running is bad", it's more "running insane distances and/or running at insanely high intensity is bad", but the issue is a lot of people who get really into running end up doing one or both of those things.
One sign that marathons (let alone ultramarathons) may not be particularly healthy is that the first guy to do one famously died, and then subsequently people die doing them every single year. Yes the risk is low overall, but that doesn't mean it's actually good for you