Although Jesus cleansed the church with his own blood, that it may be without spot or blemish, without corruption, as long as the Church functions within this evil and fallen world, it will inevitably be stained from time to time.

The parable of the weeds (or the tares) is Jesus' way of showing the truth of the Kingdom of Heaven within the fallen world that we have. The enemy will sneak in and sow corruption amidst the Church.