Yes. The Supreme Court was created as part of a system of Checks and Balances of the three branches of government. The executive branch appoints judges to the bench, but once there they are there for life unless they resign or behave badly. If the president breaks a law, it is up to the Supreme Court to check the president, just as the president can change the nature of the court through his appointees.
The Supreme Court is not an assertive branch of government as the other two branches are. That is, it cannot primarily act on its own to assess laws or actions of elected officials. If their actions are legally challenged, their role is to rule on those legal questions and their constitutionality.
In 1835, the Supreme Court rules the Indian Removal Act unconstitutional, even though it didn't stop Jackson from ordering the Trail of Tears.
I don't have any specifics in mind, but the concept of checks and balances allows the Supreme Court to keep the President (or the Congress, for that matter) from overstepping his boundaries. If something done by either the Legislative or Executive branches of government is unconstitutional, it is the responsibility of the Judicial branch to right that wrong. What the Supreme Court can not do is act as some kind of moral or ethical authority over the actions of a President. Only if a legal case is brought before them can they make a judgment which overturns, overrules, or limits the actions of a President. Even then, the case may not prevail. That's the law, and that's the American system of checks and balances.
If the president takes an action that is unconstitutional, the Supreme Court can certainly rule that his action must not continue. I can think of two examples right off the top of my head.
First, the Supreme Court ordered President Richard Nixon to turn over tapes that he had made of discussions in his office. The Court said he had to do this because there could be evidence on the tapes relating to the Watergate coverup. (This is US v. Nixon.)
Before that, the Supreme Court once ruled that President Truman had acted illegally when he took control of some steel mills back in the 1950s. This is the case of Youngstown Sheet & Tube v. Sawyer.
In both cases, the Court was ordering the president to do something.