You either live with the current results or start fighting with the contractor to jackhammer up the old floor or portions thereof and repour it.
There should be no structural reason to replace the floor and depending upon your long term plans for the basement and how badly the floor is now finished, my simply want to accept it as it is (maybe with a discount from the contractor) and deal with the issue later...like covering it with a carpet.
But as for 'fixing' the floor with a cement topping compound, it's not a very practical alternative for cosmetic as well as bonding reasons.