The Disciples Misunderstood the Bread Warning
When Jesus warned the disciples to beware of the leaven of the Pharisees, they thought he was talking about actual bread.
Matthew 16:5–12. Jesus says: 'Take heed and beware of the leaven of the Pharisees and of the Sadducees.' The disciples reason among themselves: 'It is because we have taken no bread.' Jesus responds with exasperation: they have forgotten the feeding of the five thousand (and the four thousand). 'How is it that ye do not understand that I spake it not to you concerning bread?' Then, verse 12: 'Then understood they how that he bade them not beware of the leaven of bread, but of the doctrine of the Pharisees and of the Sadducees.' The disciples required an explicit explanation of a metaphor that had just been used in a context where bread was obviously not the topic.
Red Letter Sources
Matthew 16:6Matthew 16:11
Then Jesus said unto them, Take heed and beware of the leaven of the Pharisees and of the Sadducees.
How is it that ye do not understand that I spake it not to you concerning bread, that ye should beware of the leaven of the Pharisees and of the Sadducees?
Evidence Notes
Matthew 16:12 explicitly states they eventually understood the metaphor. The original misunderstanding is in v7. The entire exchange is textual.