The reason John appeared is because it's been over 60 days and he's set to appear at that time
but don't worry
You don't have to do anything, just carry on as normal, you don't need to interact with john at all until you need to.
For now, wait until John leaves, which will be in 7 days and he'll return after 14 days, and he'll repeat that until you either kick him out or let him stay, after which you can do what ever you want, even if he's there, which would only limit you at night in the living room.
and the same thing with Danielle if she appearance earlier than you expect her to, which is after 100 days, you can ignore her until you get to her part in the walkthrough.