Article I, Section 8, Clause 9:
[The Congress shall have Power] To constitute Tribunals inferior to the supreme Court.Article II, Section 1:
The judicial Power of the United States, shall be vested in one supreme Court, and in such inferior Courts as the Congress may from time to time ordain and establish.Article III, Section 2:
In all the other Cases before mentioned, the supreme Court shall have appellateJurisdiction, both as to Law and Fact, with such Exceptions, and under such Regulations as the Congress shall make.The jurisdiction of the federal courts are subject to the regulation of Congress. Congress can pass a simple law stating that classes of cases (other than those described in the Constitution) do not fall under the jurisdiction of the courts.
President Trump is right on this one. Bathroom regulation is not a federal issue and should be left up to the states, local governments and school districts.