For me it comes from:
Bad fit. Calves are probably stretching which means seat too high. That's the opposite of what most people do though. So it may be worth asking someone to take a look before fiddling too much.
High gear. Either I'm just grinding a high gear for speed (finally got my cadence meter placed right so it registers!) or I'm climbing and not downshifting enough. Either way riding on too high of a gear gives me calf spasms that can last for days. And since I have tendonitis on my left achilles I need to avoid that like the plague already.
Too much too fast. Similar to high gear. You're just pushing your body hard. Maybe not adequately fueling for long/hard rides. Are you drinking enough? Getting enough electrolytes (especially potassium)? Enough sugar during the right to prevent crashing and eating properly before and after? Are you drastically increasing your max distance? Stringing together numerous long rides without enough rest? Normally I try and only add 5-10% to my max distance in one go (going to ignore that this weekend since riding group is doing a ride that looks like fun that I want to tag along with).
Not helping my body heal. Most days I have oatmeal and coffee for breakfast. On long ride days I add in some eggs and sometimes a strip or two of bacon. After the ride, lots of chicken and a bit of rice. If I don't eat right before/during/after a long ride I recover far slower. Also I bring homemade energy gels and sometimes coconut water with me for long (or hot since summer is coming which means 110-120 degree days are on the way). I try and stretch often after long rides (using stretches similar to ones I used to help me tendonitis in the past). I also get my wife to use a roller on my calves, quads, and sometimes arms and lower back. Some days I make myself go for a 1-5 mile ride the day after a long ride just to help with the recovery. Other than that, I rest until the pain is gone.
When I first started pushing mileage I'd be in pain for days after the fact. The worst was a muscle cramp on a charity ride going uphill. I was so tired that I walked my bike up the last bit of hill and the leg locked up. I had to lean on my bike just to keep walking. Thankfully I was able to coast downhill after that and was able to use my pedal and hand to massage the calf and barely finished. But I was limping for 3-4 days after that. Nowadays when I feel pain (not fatigue but actual pain) it is less sharp and goes away way faster. Part of that is just reducing the chance of hurting myself. Part I assume is that my muscles can just take more abuse nowadays.