The most common cause of failure, is dead shorting/arcing between the cell gap and the mod tube/case. Especially if the batteries are loose in the case (undersized). I always recommend that someone use a PVC or cardboard sleeve to keep the cells aligned. The simple solution it to just wrap the "stack" in tape. It's not pretty and takes a few seconds extra to do (during a battery swap), but does provide SOME added protection.
Also check your cells with a voltmeter when they come out of the tube (for recharging). If you see a cell gap (difference in voltage between the 2 cells) of more than 1/2 volt or so...then something is wrong. You could try fully charging the cells, one at a time, on individual charging legs (multi cell charger). If the cell gap is still there, then the problem could be the charger. If the gap is under 0.2 volts when the cells are peaked (fully charged), but they come out of the mod with a much larger gap than that....chances are you have a damaged/tired/worn cell.
The suggestion of rotating cells (in multicell configurations) is a good one. It is also helpful to give the cells a chance to "settle" once you take them off the charger. They will last much longer.