Absolutely. Greninja frequently bubble their young to make them comfortable, to protect them from harm, or to keep them warm. Assuming you live in the northern hemisphere, it’s currently autumn, going into winter, which means the temperature is dropping. Your greninja is likely preparing for this. In addition, the unusually warm temperatures we experienced through the summer may explain why you’re only noticing this recently—because it wasn’t as needed a few months ago.
Alternatively, some greninja subspecies bubble their young to teach them how to create bubbles themselves. By surrounding them with bubbles, the greninja forces her young to watch her as she creates the nest, so they can figure out how to weave their own later on in life.
In short, so long as your froakie can breathe and stay moist, they shouldn’t be in any danger.
The Pokédex According to Bill 