There is a correlation between running, and lower back pain, with symptoms that don't always present in a logical place. Recently, I experienced unilateral pain in my right quadricep - or, my right quad was a lot more tired/sore than my left quad - despite massage, foam rolling, and stretching.

Pain in this area can indicate a problem around L2/L3 of one's spine: possibly a bulging disc.

This page has a good diagram:

TL;DR? Unbalanced pain after exercise? Look further than the site of the pain: it could be referred from elsewhere. Ask your physiotherapist about referred pain, or book an appointment with a doctor.