How come my puppies keep crying when left alone with each other?

We’ve had our 2-month old puppies for seven days now, and they’ve been doing fine until today. We keep them in a stairway next to the kitchen, so that it allows them to go up and down. But they keep going to the second floor, which has a door that leads them to our rooms. They have a small case of kennel cough, so is it a side effect? I’m worried because they have not cried like this before. It’s kind of weird!