There are several reasons why this can happen.
(See figure) When battery A (high electrical capacity; not yet drained) and battery B (low electrical capacity; nearly depleted) are discharged in series, battery A will still have a lot of remaining capacity whilst battery B is near depletion. When this is the case, it is possible that battery B will be further discharged by forced current from battery A. In this case there is the possibility that battery B will get a negative voltage. This can happen when there is a mixed use of old and new batteries together. If this happens the likelihood of leakage will raise, so please take out and dispose these batteries.