Both are correct, but the focus is slightly different. "In" refers to the interior of an enclosed space. "In the café' means INSIDE the building - it is the opposite of outside the café. For example, "We waited in the café until the rain stopped.". "At" is a general location, or a point in a journey. We spend time at various locations in our daily lives - at home, at work, at school, and 'at the café/pub/library/gym' is one of those locations. For example, you might say "It's too crowded at the station - let's meet at the café instead". This doesn't refer to a physical interior space - "at the cafe" could mean inside the building, but it could equally mean that you are sitting on the terrace outside the café, or even standing in the street in front of the café. And, of course, if you're talking about an outdoor café in a park, for example, you can only use "at".