I think of calves separately from the rest of the leg. Unless you're one of the genetically blessed calf dudes, just throwing them in at the end of a leg workout isn't likely going to give you the aesthetic look to match the rest of your physique. Like it's fine to do that, but have other days where calves are the first thing you do before you expend all your energy. And consider doing them up to 3x a week sometimes. I typically try to hit them on days I do cardio, since doing cardio the day after any leg workout doesn't really work lol
As far as injury from leg extensions, running, etc: listen to your body. I've been in this game a while and at this point I feel I've learned to separate the kind of pains where I know I need to pull back or use moderation from the ones it's okay to work through. Don't forget adequate recovery is one of the most important parts of any effective physical fitness program