Let's work through the Sugya according to the Tiklin Chadtin and answer your question in the process.

To answer the question what size boxes is one permitted to clear out of one's storehouse on Shabbos, the Gemara cites the Beraisa, which refers to filling three boxes each holding three Se'ah (nine in total), from the large box containing all the Shekalim, on each of the three occasions that the Terumah was taken during the year (in which case, the large box must have held twenty-seven Se'ah altogether, as the Tana points out).

The 'Masa di'Yerushalayim' explains, that the fact that the Tana adds the first total of nine Se'ah, and the second total of twenty-seven, is to teach us that it means exactly three Se'ah and no more (because if he took more on one occasion, there would not be enough for the subsequent Terumos). That explains why the Gemara finds it necessary to cite the Beraisa and not the Mishnah to resolve its question, since the Mishnah can be interpreted as 'Lav Davka' (i.e. a minimum of three, but more would be permitted).

Eliezer Chrysler