Federal courts have jurisdiction over issues that arise between states because Article 3 of the Constitution specifies that all controversies between two or more states are federal responsibility.
Earlier some problems with Interstate Disputes (of lands, natural resources as water and gas or economics issues) required Federal Court decision, so the Article 3 of the Constitution specifies that in cases involving “controversies between states or between the U.S. government and foreign governments” the Federal courts will have jurisdiction over it.