Joseph insists that they are spies, though they deny it, and though he knows they are speaking the truth. He accuses them to stir up their consciences.
Although this had happened many years before, the conscience is able to bring our sins to full remembrance long afterwards. It does not fade with time. It was affliction that brought their conscience to life, for they thought now that they were under the judgment of God and search their hearts for why this should be, and it was not hard for them to remember their sin. God will use affliction on us to help us practice self-examination of the sort that we are not normally willing to practice. Conscience never gives up. Though we may shut out its accusations now, we will have to face them one day, possibly before the judgment seat.
Christ too makes himself an accuser of our souls when he first deals with us. He addresses us with his law and awakens our conscience to condemn us, so that we despair of life. We are so unwilling to acknowledge our sin that the law must be applied to us to prove what we would rather deny. The Holy Spirit must take the law and convince us that any idea that we could ever be acceptable to God on the basis of our good works is groundless.