Yes, the running hits the calves hard. That's probably it. Too much/overwork.
I've been using a scrap piece of 2x12 to do my calf raises on. I do them in my power rack with a barbell on my shoulders as I don't have a standing calf machine.
A friend of mine had a knee replacement a couple weeks ago by a top surgeon. Guy told him jogging is the worst thing you can do for your knees. He said it just pounds your knees. Said all these people jogging are wrecking their knees. However, he said running fast is ok. Just no jogging because of the pounding.
Running on hard surfaces, even walking on hard surfaces can be tough on knees.
I don't believe avoiding exercise is the right prescription for avoiding ruining your joints. We all know people that have never done anything physical in their life that need knee and hip replacement.
At the other extreme are those who exercise too much. I believe Paul Anderson, Clarence Bass, Lou Ferrigno, Grimek and many others have had hip replacement surgery. Maybe squats are bad? Thinking about doing body weight free hand squats. Wilf Sylvester won the short class Mr. Universe in 1975 giving up the barbell squat. For that contest he did 400 reps of body weight free hand squats with leg extensions and leg curls. Not sure if it was one set or several to get to 400 reps.
I think grinding heavy lifting is worse than using a more moderate weight for volume. I could be wrong. Look at Chris Dickerson. He always trained with volume and moderate weight. His knees, back and hips are completely shot but he also did Olympic lifting when the AAU wanted Athletic points to compete in bodybuilding.
I think the majority of pure runners have healthy joints. Having come from a competitive running back ground I know guys that have run hard for 50 years. I know one thing for sure. My shoulders that I thought were bullet proof started giving me trouble when I reached around 55. My knees that have never given me a bit of trouble are acting up. I blame the leg press machine in the commercial gym I train in. It's not built right and I think it's grinding my knees to dust. I stop using it. I only use the leg press machine in my home gym. It has the right angles and it's smooth. If my joint issues continue I will go to volume with a more controlled cadence. I still deadlift and my lower back is bullet proof knock on wood. If that goes I might go to moderate weight power cleans for higher reps like 6 reps.