Mark 8 is one such example -
14 Now they had forgotten to bring bread, and they had only one loaf with them in the boat. 15 And he cautioned them, saying, “Watch out; beware of the leaven of the Pharisees and the leaven of Herod.”  16 And they began discussing with one another the fact that they had no bread. 17 And Jesus, aware of this, said to them, “Why are you discussing the fact that you have no bread? Do you not yet perceive or understand? Are your hearts hardened? 18 Having eyes do you not see, and having ears do you not hear? And do you not remember? 19 When I broke the five loaves for the five thousand, how many baskets full of broken pieces did you take up?” They said to him, “Twelve.” 20 “And the seven for the four thousand, how many baskets full of broken pieces did you take up?” And they said to him, “Seven.” 21 And he said to them, “Do you not yet understand?”
I had always read this passage and been like "umm, actually Jesus, no I don't." I didn't understand the talk of the leaven of the Pharisees (though I knew it was bad), nor did I understand why Jesus was saying these things. What prompted this? I had always thought Jesus was saying "why are you discussing the fact that you have no bread" because there were more important things to worry about (like the fact that the very Son of God was going to be crucified at the hands of men!), but that explanation never really fit the context, so oftentimes I was just perplexed.
But as I kept reading this passage, something clicked, and it really was just a lot simpler than I thought.
They don't have bread, and what was Jesus rebuking them for? Not believing that He could provide. He provided for the crowds (twice!) and he could provide for them. Beware of the leaven, the unbelief of the Pharisees. Do you not see?
If Christ could feed so many, why are you so worried about not having bread for just the twelve of you?