The very same thing happened to me yesterday, I was about to charge a 3 cell 11.1v lipo but had the charger set to 2 cell, (2s), 7.4v, it warned me of my error straight away, clever things these lipo chargers.
If you were mention some details of the charger you are using and the battery you are charging it could be that someone has had the same problem with that particular charger / battery.
All the best
Neil