The disciples had forgotten to bring bread, and they had only one loaf with them in the boat. Jesus enjoined them, “Watch out, guard against the leaven of the Pharisees and the leaven of Herod.” They concluded among themselves that it was because they had no bread. When he became aware of this he said to them, “Why do you conclude that it is because you have no bread? Do you not yet understand or comprehend? Are your hearts hardened? Do you have eyes and not see, ears and not hear? And do you not remember, when I broke the five loaves for the five thousand, how many wicker baskets full of fragments you picked up?” They answered him, “Twelve.” “When I broke the seven loaves for the four thousand, how many full baskets of fragments did you pick up?” They answered him, “Seven.” He said to them, “Do you still not understand?”
The Lord indeed abandons the Pharisees, as men uncorrected; for where there is a hope of correction, it is right to remain; but where the evil is incorrigible, we should go away. There follows: Now they had forgotten to take bread, neither had they in their ship with them more than one very loaf.
By a special providence also the disciples forgot to take bread, that they might be blamed by Christ, and thus become better, and arrive at a knowledge of Christ's power. For it goes on, "And He charged them, saying, 'Take heed, and beware of the leaven of the Pharisees and of the leaven of Herod.'" He means by leaven their hurtful and corrupt doctrine, full of the old malice, for the Herodians were the teachers, who said that Herod was the Christ.
But the disciples themselves thought that the Lord spoke of the leaven of bread. Where it goes on, "And they reasoned amongst themselves, saying, it is because we have no bread;" and this they said, as not understanding the power of Christ, who could make bread out of nothing. The Lord reproves them; for there follows, "And when Jesus knew it, he said to them, 'Why reason you because you have no bread?'etc."
Catena Aurea (St. Thomas Aquinas)
Explanations on the New Testament (St. Theophylact of Ochrid)