Welcome, myshka!
He is a baby, and may be pottying in his pouch. Is it only in the bonding pouch, or both? Neutering won't have anything to do with this. I don't think there is anything wrong, but I'll wait for other opinions, and the answer to the question.
Have you tried giving him a little time outside of his pouch before he goes into the bonding pouch.
What is babies name?
Also, can you put your name in your signature?