How old are they?
It sounds to me like they are just starting to lose their baby teeth. I know that when our puppy starting losing her teeth, it seemed like they all came out at once! When puppies start to lose their teeth they definitely have some severe bad breath, so that could be what you are experiencing.
I agree with Chillipepper though, if something was seriously wrong I would imagine that your vet would have said something. If you are still worried, a call to the vet never hurts just to make sure.
__________________  Proud Parents of Maci and Jaxson    RIP Jaxson (4/22/2016) |