When someone has a will, it only controls what is in the estate. There are many things that pass outside of the estate and therefore are not controlled by the will. Any that has a beneficiary on it is not part of the estate. That can include retirement accounts, life insurance, brokerage accounts and even bank accounts. Anything that is co-owned (with some exceptions) also passes outside of the estate and is not controlled by the will.
Your father's will technically did not control either of the bank accounts because the accounts were co-owned. Therefore legally your brother wasn't entitled to any of the second account either because the will did not control that account, despite the fact that your father included it in the will.