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In Chapter Twelve of Philosopher's Stone the following sentence appears:

"And you're not sitting with the prefects today, either," said George. "Christmas is a time for family."

It appears from this sentence that the rest of the year (i.e. besides Christmas) the prefects sit separately from other students. I am trying to figure out what this is referring to.

I know that there is a special prefect carriage on the Hogwarts Express. From Philosopher's Stone Chapter Six:

"Can't stay long, Mother," he said. "I'm up front, the prefects have got two compartments to themselves —"

And from Order of the Phoenix Chapter Ten:

"We’re — well — Ron and I are supposed to go into the prefect carriage,” Hermione said awkwardly.

And from Half-Blood Prince Chapter Seven:

"We can't, Harry," said Hermione, looking apologetic. "Ron and I've got to go to the prefects' carriage first and then patrol the corridors for a bit.

However, George is clearly not referring to the Hogwarts Express. They don't go on the Hogwarts Express that day, and they have not been on it for nearly four months at this point. George is obviously referring to some more recent occurrences of Percy sitting with the prefects as opposed to his family.

I also know that there is a prefect bathroom. From Goblet of Fire Chapter Twenty-Three:

"Tell you what," Cedric said, "use the prefects' bathroom.

And from Half-Blood Prince Chapter Six:

"That gives you equal status with prefects!" cried Hermione happily. "You can use our special bathroom now and everything!"

But it is also pretty clear that George is not talking about which bathroom Percy uses.

So what is he talking about? What else is there where prefects sit separately from other students? I would have assumed that it might be referring to sitting in the common room, or sitting in the Great Hall, but as far as I know there is never mention of a special seating area for prefects in either of those locations. And if we are to assume that it means that the prefects simply unofficially sat together, there are other occasions where we see Percy sitting with the others both in the Great Hall, and in the common room. From Philosopher's Stone Chapter Seven:

On Harry's other side, Percy Weasley and Hermione were talking about lessons

From Chamber of Secrets Chapter Nine:

Harry, Ron, and Hermione chose seats as far as possible in the common room that night.

(Implying that otherwise, prefects and regular students sat intermixed.)

From Chamber of Secrets Chapter Fourteen:

Percy Weasley was sitting in a chair behind Lee, but for once he didn't seem keen to make his views heard. He was looking pale and stunned.

From Chamber of Secrets Chapter Sixteen:

"If you've finished eating, I'll take that seat, Ginny. I'm starving, I've only just come off patrol duty."

Ginny jumped up as though her chair had just been electrified, gave Percy a fleeting, frightened look, and scampered away.

From Prisoner of Azkaban Chapter Eleven:

Ron and Hermione watched Harry nervously all through dinner, not daring to talk about what they'd overheard, because Percy was sitting close by them.

And, of course, once Ron and Hermione became prefects they continued to always sit with Harry in the Great Hall and the common room.

So what phenomenon involving Percy sitting with the prefects was George referring to?

George is talking about Christmas dinner.

The house prefects would normally all sit together at regular mealtimes throughout the year, so George is telling Percy that he should sit with family and not friends for Christmas.