And he didn't quite say that the judiciary can't check the executive. He said that the judiciary can't check the "legitimate power" of the executive. (Of course, that completely misses that the judiciary checks the executive precisely by ruling that something is outside the legitimate power of the executive...)
That's where the battle line is currently drawn. Does the president get to decide that, or does the judge? Is it a fig leaf, or is it a real constraint?
There fundamentally is going to be conflict in any system of checks and balances. Neither the SCOTUS nor POTUS get to unilaterally decide the limits.
Trump hasn't been following convention, but that doesn't mean he's wrong. We also can't just assume he's right. Having the 3 branches hash out a balance is perfectly reasonable and confirms the system is working as intended.
And he didn't quite say that the judiciary can't check the executive. He said that the judiciary can't check the "legitimate power" of the executive. (Of course, that completely misses that the judiciary checks the executive precisely by ruling that something is outside the legitimate power of the executive...)