Why does Mrs. Mann punish the children when they complain of hunger?

Mrs. Mann's punishing the orphans when they ask for more food has less to do with discipline and more to do with covering up her own embezzling. She takes for herself some of the funds allotted to the upkeep of the orphanage. The last thing she needs is an orphan calling attention to their lack of nutrition by asking for more food.
The orphans are also guilted into silence, even by the officials outside of the orphanage. Later on, when Oliver is brought before the Board, one of the gentlemen present tells him, "[I hope] you pray for the people who feed you, and take care of you, like a Christian." The men of the Board accuse Oliver of ingratitude when he betrays the least bit of misery. When they learn Oliver has asked for more food, one even suggests he is doomed to become a criminal when he grows up—he must be greedy if he wants more.
When Oliver asks for more food, he is indirectly calling to attention just how bad the orphanage is. His request not only puts Mrs. Mann in danger of being prosecuted, but it also criticizes the state for its treatment of the unfortunate. This is what leads to the overreaction from the adults in charge.

Oliver Twist’s mother dies right after he is born, and he is placed in an orphanage. Mrs. Mann runs the orphanage, and even though she is given ample money to feed the children, she keeps most of the money for herself and barely feeds the orphans. She does not care if they starve, and when orphans die, she covers up their deaths and say it was an accident. When the children complain about being hungry, they are punished. When Oliver asks Mrs. Mann for more food, he is placed in solitary confinement. Mrs. Mann does not want the children to complain about being hungry, because she does not want anyone to find out she has been stealing from the orphanage.