while they may not technically have a belly button, animals that hatch from eggs do have an opening in the abdomen wall where the yolk is absorbed through. The last of which is done within hours of hatching for chicks. In chicks, this is a mechanism to help them while their nest mates hatch over a period of several hours to a day. It enables them go be able to go for approx. 24 hours before needing to be fed. I'm not sure for reptiles if it works the same, but the yolk is attached in the same manner. This area is normally closed entirely before hatching, but occassionally it has not yet completely absorbed or closed, thus leaving an opening in the abdomen. But, after a day or so, it should close and cover over with skin if properly cared for and kept moist so it does not dry out.
This could be the remnants of a poorly absorbed yolk or the area not closing properly. It could be somethiong entire different. I'm basing my reply on my knowledge and exprience in hatching chicks.
I hope you find out what it is, - maybe a trip to a vet is warranted.