Muscular imbalance due to poor habits (such as a forward head or improperly aligned asana) or repetitive movement patterns (such as typing on a computer, carrying children or lifting heavy items).
Other musculoskeletal conditions such as one shoulder higher than the other or rotated forward, one scapula pulled in more than the other; the head leaning to one side, and/or a flattened cervical curve. (Gary Kraftsow, Yoga for Wellness p 143)
The most common rotator cuff injury is to the supraspinatus which, Doug Keller notes here, can happen through overdoing such common poses as Down Dog and Side Plank or in advanced arm balances such as Firefly. Other causes are accidents and repetitive actions.
Note
There are many muscles potentially involved in shoulder and upper back issues. For instance, while pain may be felt in the upper back caused by the shoulder blades being pulled away from spine, chronic tightness in chest muscles can be a causal factor.
