My dog (who is not a puppy) does some strange things and makes some weird noises during dreams and sleep. She howls, moans, yips, breathes like she's running a marathon, snores...... So weird breathing CAN be just a dreaming-thing. The length of time it takes to really "wake up" can vary with dogs too. Mine wakes instantly, but some dogs are dozy for a minute or two after waking.
I would say that if she was having seizures of some kind, you would be likely to see the symptoms at other times...for instance when she is awake as well. But obviously, if she does show these "episodes" at any other times, shows any other symptoms of being unwell, or you are really worried, take her to the vet.
It is quite possible she is dreaming and when You wake her up she is still confused. Dogs dream and it does happen with a lot of them especially Puppies. We have a 6 month old pup who has done it since we adopted her she goes into a deep sleep and growls etc, heavy breathing and is in a daze after she even wets herself. She has been to our veterinarian numerous times and I myself also work in a veterinarian clinic where I have seen a few. If You're concerned take her to your veterinarian but is sounds normal
Sometimes puppies can really sleep hard,But from the way she was acting a few days ago it sounds like she may be having some neuro problems or maybe her blood sugar was really low.If it is her sugar then they usually out grow that.If she acts odd like that again then you could try giving her some Caro syrup and that helps get ther blood sugar back up again.Alot of times with Hypoglycemia they can do what you said she was doing.What breed is she and how old?It would probably be a good idea to call your vet and tell them what is going on and see what they think you should do.I hope that she gets feeling better soon.Keep us posted.Take Care