During in utero development, some "mistakes" can happen.
One of the kidney will have tissue formed normally, but the size will be smaller than the normal size of the other kidney, and the smaller kidney is known as a hypoplastic kidney.
Sometimes, kidney tissue forms poorly and forms a scarred and poorly functioning kidney, known as renal or kidney dysplasia (this kidney eventually shrinks
down).
hypoplastic kidney, usually, is dysplastic at the same time.
Is it possible that your child had a faulty drainage system in one kidney leading to reflux nephropathy (kidney is damaged and becomes smaller)
Someone with reflux nephropathy can have a sever case of kidney infection, and this infection can damage the kidney, making it smaller.
Also, another more serious cause for smaller kidney is a kidney tumor, known as Wilms' tumor (the tumor mass often distorts the kidney and can compress normal tissue into a thin rim; It may cause bleeding in the kidneys and urethra, making the urine bloody).