If you are legally able to claim deductions, pre-filled tax forms that do not contain those deductions are by definition wrong, even though you may agree with individual form items. While this can be related to innocent mistakes and the sheer inability of the state to know the necessary information, sometimes it appears to be deliberate: The classic example is the Pendlerpauschale, which does not appear in Elster pre-filled tax forms even though the state does have all necessary information (address of your flat / address of your employer) to fill it.

If you accept these faulty forms, you will almost always pay more taxes than you have to.