Possibly the saddle too high causing the calf area to in effect “over-reach”. You would probably find some knee soreness/ ITB soreness if this was the case though…
Most likely seems the alignment of your (hip, knee and) ankle as you look at the bike front on could do with a bit of closer inspection. Keeping everything in a line is the general recommendation but it isn’t always as simple as that. If your knee does not track straight it might not be bad and equally strengthening the muscles around the knee might not be any help. Tightness in the hip and back could give issues which transfer down to the ankles as could a multitude of other factors.
What pedals? I have found Crank Brothers Eggbeaters to be particularly poor at giving any support which might irritate old niggles.
Generally speaking a cleat position further towards the heel reduces the contributions made by the calf during pedalling which is an extreme option to tests perhaps.
Basically…. it could be any number of things and I doubt anyone here will be able to solve this. Best bet is to see a physio I would say