I heard that cracking sound on Missy before too so I mentioned it to her vet at one of her apt.s and he checked her back legs by placing his hand on her back leg and moving it down gently so the leg straightens. He found one of her legs pops when it straightens, the condition she has is called Luxating Patella and it can be common in small breeds. I haven't done much research on it so I cant offer you anymore, but maybe you can check his back legs to see if that's where the cracking sound is coming from.
If that's not it I have no idea what it could be, but I doubt your baby is breaking
