Stopped at immigration

The incident happened recently when I was coming back to india from Thailand with my wife. I was stopped at immigration while my wife got through with the process. They made me wait for an hour before sending me to customs to check my bags thoroughly. Nobody was ready to give me any clear answers. After I got cleared after hour and a half later, I went to the immigration myself to enquire about the incident. Literally, no one among those three employees had any clear answers to my questions. All I got was that my passport was flagged as 'refer to customs' or something like that. So I came here, to know if this is a common thing that happens or for specific reason. Please do share if anybody knows something about this.