Thankfully there are steps we can take to "un-fuck" (that's the scientific phrase) the damage that people are doing to their bodies out there, mile after mile. The things that happen to runners aren't, for the most part, unique. They are things that we can plan around and either correct or attenuate. Let's discuss.
1) Think posture! Runners posture ends up looking a lot like the posture of someone who sits at a desk all day...which most people do. Awesome, so they get shitty posture sitting at their desk and then compound it by going out and knocking out a 5-miler at the end of the day. Their shoulders are internally rotated and their thoracic spine is stuck in flexion with protracted shoulder blades. A big focus during the warm-up/mobility portion of the session should be on improving thoracic spine extension and scapular mobility. This focus will get someone a lot of bang-for-their-buck. They'll see improvement very quickly, and it will make a difference in the way they look, feel and move.
2) Get them strong! Each stride a runner takes is a sub-maximal uni-lateral effort. They produce low power at a low-level of strength with each leg for hundreds/thousands of reps. The main component of their strength training routine should be heavy (fewer than 5 reps) bilateral lower-body exercises. I would prefer a focus on hip-dominant exercises (deadlifts, low-bar squats) with a spattering of knee-dominant squats as assistance work. Runners tend to have weak hamstrings and we need to bring those up so we can improve performance and get rid of any knee pain that is (probably) present. Plus, strong people are harder to kill than weak people.
3) The hips don't lie! Pelvic stability is a huge issue for runners, especially female runners. All those strides cause some pretty swishy hips, which can lead to some very uncomfortable hip and low back pain. In order to prevent/fix this, we need to train pelvic stability. There are two planes of motion that we want to train the pelvis: sagittal and coronoal (front/back and left/right). The common ways to train the pelvis to be stable anteriorly/posteriorly is with bridges and planks. These are ok for teaching pelvic stability, but with a more advanced athlete you'll need something better. Barbell-loaded hip thrusts and ab-wheel rollouts are a great idea, as are some of the pallof press variations. Your butt muscles are very important pelvic stabilizers and they need to be heavily trained and activated in runners. Remember: no glutes, no glory!
Another great way to teach this stability is by using loaded carry variations. Personally, I would like to see runners do a lot of anterior-loaded (goblet position) carries, along with some offset loaded carries (DB on one side). This will also help someone learn how to control their pelvis laterally, by activating their obliques and their quadratus lumborum, one of your biggest trunk stabilizers. Most of these exercises will also train the anterior core musculature, which will benefit a runner greatly by helping to stabilize the whole trunk during a long run.
4) You can never underestimate the importance of soft tissue quality! Runners put a lot of repetitive stress on their muscles. This leads to tightness and poor tissue quality in a few specific spots. Having your runners doing a lot of self-myofascial release is going to help alleviate a lot of discomfort they may experience. Get them to focus on the bottoms of their feet, calves, IT bands, quads and upper back. Using both the foam roller and lacrosse balls will help get to all those gnarly little trigger points that are limiting your range of motion anywhere. Excessive stretching of the lower body is usually not recommended for runners since that tonicity (especially in their calves) helps propel them along at a faster rate.
5) Train them in 360 degrees! Runners live in one plane of motion; straight forward. Other than dodging the occasional pile of dog poo or a pedestrian, there is very little lateral movement involved in running. Get these people moving as we were intended. Involve lateral lunges, side step-ups, Heidens (skater jumps), lateral sled drags and even lateral footwork with a speed ladder. Absolutely anything you can think of that will get runners moving in different directions. As we know, if you repeat anything enough times you will create an imbalance. Every stride a runner takes brings them once step closer to these imbalances.
Obviously, every runner you encounter will have slightly different imbalances; there's no such thing as a cookie cutter training model for any athlete. However, these 5 things outlined are good places to start. Will some runners avoid this all-together? Sure, but they are the exception not the rule.
You will also notice that I managed to keep my opinion to myself regarding running. I often make it seem like running is the worst thing in the world (for me, it is) but in reality it really isn't so bad if you take the proper precautions. My big beef with running is when people use it for weight loss rather than as another form of exercise. I also didn't delve into stride mechanics as something to consider with runners because, frankly, I don't know enough about it. For something like that, I would outsource to a good running coach. If you're going to run, then go for it. But make sure you do some sprints and lift some heavy shit too!