פירוש על קידושין 66:6

This story seems to prove that a son should always stand before his father, for Shmuel instructs R. Judah to stand in front of his father, even though his father was his son’s student.
The Talmud rejects this argument—R. Judah was not told to stand in front of his father because of his father’s scholarly characteristics. It was his father’ good deeds that caused Shmuel to rebuke R. Judah for not standing, and even other sages stood in front of him.
What Shmuel was telling him was not just to honor his father. He was telling him to honor his father even at Shmuel’s expense.