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: http://www.pt360atl.com/2016/08/02/referral-patterns-sacroiliac-joint-facet-joints-myofascial-system/
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.