Hi, many thanks for the query!
A kidney cyst
may sometimes cause pain & if its very small in size (as in your case), need not be removed surgically, just pain killers would suffice.
Also your urine report is good so need not worry.
In future, if episode of pain occurs, get an USG KUB, urine (R/M) done & if normal then can take pain killers symptomatically with your doctor's opinion.
Wish you a good health.