The phrasal verb here is simply "call in", meaning to make a brief, casual or unscheduled visit to a particular place. For example, "I'm going to call in at the office on the way to the airport." The word "for", followed by a noun, indicates the reason for the visit. For example, "I'm in the office all morning. Why don't you call in for a chat?".

It's a question. Why don't you come, to where I am currently, and have a coffee with me? Generally it means at your home or office. But it could me to the place where you are staying eg. a hotel.