At worst, you will be taken to secondary inspection and grilled about whether you have acquired a foreign passport. If there is no evidence of wrongdoing beyond something as simple as a missing stamp and the computer records match up with your boarding pass, you will probably be out of there in 5 minutes or less. Chances of this even happening however are very slim. Most interactions of Indian passport holders with Immigration nowadays are no more than a few seconds with zero conversation.

I'm actually surprised however that this happened in the first place. The last couple of years in Mumbai, they have a secondary passport check at both arrivals and departures where they ensure that every passenger has received a passport stamp to avoid exactly this scenario. Is it possible that your passport has been stamped but somewhere where you can't find it easily (on top of another stamp/visa, corner of page, etc..)?