The court passed a judgment stating that they are entitled to a right in the property for their legitimate share in the ancestral property, which is not disputed.
If your father is stated to have maintained the property all these 20 years, it can be seen that he maintained the property out of his own expenses to enjoy the property in a proper and habitable condition.
As a matter of fact he is liable to pay rent towards the share of your aunt for having occupied and enjoying their share in the property for all these 20 years or more.
Moreover there was no compulsion on him to spend towards the maintenance of the property but he undertook the same on his own just for the reason that this property belongs to him. Now when the court has passed a judgment stating that his sister is also entitled to a share in the property you are talkng about the share in the liability.
Besides, your father in his written statement has totlally denied their allegations and was bent upon to refuse their rights in the property for the reasons he relied upon through his averments/pleadings made in the written statement.
He might have mentioned that he had been in possession and enjoyment of the property all these 20 years hence her claim is barred by limitation. He also would have averred through his pleadings that he spent towards the maintenance of the property, but did he claim a share out of the so called liabilities ?
Without asking for a share towards the liabilities or the maintenance expenses, the court will not grant any relief.
Therefore you cannot blame court for not granting the relief that was not sought.