How should one deal with a manager at work who wrongs and deprives some employees of their rights while treating others kindly?

The official should be advised and reminded of Allah so that he returns to the truth, treats those under his authority well, and rules with justice, as Allah Almighty says: (And let not the hatred of a people prevent you from being just. Be just; that is nearer to righteousness). If he does not respond, then one can complain to someone who will give you justice and supplicate against the oppressor.