Why did the urinalysis test did not detect that i have small stones in my kidney?

That in not what the test does. A urinalysis shows what is found in pee you shed, not stones attached inside the kidneys. You must do the proper study to assess the specific problem.

Urine test (urinalysis) can give some hints that a person may have kidney stone but it is not specific. Those hints are: blood in the urine or heavy oxalate crystals in the urine sediment. For clinical impression, if you have kidney pain (renal colic) + blood in urine + heavy oxalate crystals, nephrolithiasis is likely then 100% correct diagnosis if stone is detected by KUB, ultrasound or CT scan.

No test is !00%. For example If the stones are not in the area where urine is collected (imbedded stones) RBC in urine, which indicate stones, would not be seen.