More specifcally, it was the VOLUME of the yawn he commented on. Which is the one thing about a yawn that is quite controllable in most circumstances.
From the way the report reads it sounds like the judge was questioning WHY he yawned.
No he didn't question why at all. The potential juror volunteered the "why".
Should he have LIED?
No. He should have been courteous, which means apologizing without making excuses. "I apologize your honor" would have been sufficient. No need to say more.
Besides, you know darn well that much of this hinges on the tone and overall attitude of the juror, which is something that neither you nor I can divine from a written news article. If I were in the courtroom I might feel differently.