You have the problem identified - small puppy, young child, either of them could have weeed on that area and its gone deeper down then you machine is capable of pulling up.
I had a problem last year though the lady swore blind her dog had not been in that room, but i reckon it had. Was only when I gone that the smell appeared, and I was using a truckmount, so strong suction.
Just cleaning it again wont do much in my opinion.
What I did was flush just that area with M-Power/Nemesis, then used Bio Green by injecting it into the carpet at various positions of the smell area as well as spraying on top of the carpet.
Bio Green does not mask the smell, it gets to the source and eats it up. Takes time and in severe cases may need re-treatment.
I am sure other guys can recommend something similar to Bio Green cause I not seen it for sale recently