Where are you? I'm at the store.
Where are you? I'm in the store. (I'm physically in the store).
Both are correct.
At = always location, always a specific time (at home, at the store, at the beach, at 4pm, at 3:30, at 1:10, etc)
In = within something, within a period of time (In the box, in the refrigerator, in the car, in the room, in the beginning, in the past, in the afternoon, in the morning, in the evening, in the 1800s, in the 1900s, etc)