What shall we say then? [Is there] unrighteousness with God? God forbid.
Note 7 at Ro 9:14: Paul was seeking to stop anyone from interpreting his statements in a way that would make it look like God was unfair in His dealings with man. God can extend mercy to an individual without treating others unjustly. Just as in the parable that Jesus gave in Mt 20:1-16, God treats everyone fairly, but to some He chooses to give extra mercy. Does that mean He is unjust? Not at all.
If God chooses to call individuals to account for their actions and choices they have made of their own free will, He is completely justified to do that at any time. In Lu 13:1-9, Jesus mentioned the people whom Pilate had killed and mingled their blood with the sacrifices, and the people on whom the tower in Siloam fell and were killed. He raised the question (Lu 13:2 and 4), "Were these people worse sinners than others to suffer this judgment?" He answered His own question by saying that all of them deserved such judgment, but God in His mercy had spared them (see note 2 at Lu 13:2).
He then immediately followed that with the parable about the man with an unproductive tree in his vineyard. He was going to cut down this dead tree and replace it, but the vine dresser interceded for the tree. The owner then gave him some extra time to see if he could revive it (see note 1 at Lu 13:6). Likewise, people all deserve judgment, but through things such as the intercession of others, God will sometimes show extra mercy to certain individuals.
However, if He chose not to extend mercy to anyone and He called everyone's accounts due, He would be completely justified in doing so. It's His choice. God has never brought judgment on anyone without being righteous in doing so. Likewise, He has never extended mercy to any individual that made His treatment of someone else unfair.