A well-known Halacha requires covering the bread on the table before reciting Kiddush. The reason for this requirement is that normally, the Beracha over bread is recited before the Beracha over wine (since grain is listed before grapes in the Biblical verse listing the seven special species). On Shabbat, however, it is forbidden to eat before reciting Kiddush, and we must therefore reverse the order and first make Kiddush over wine before reciting Ha’mosi and eating the bread. In order to avoid "embarrassing" the bread, which is accustomed to receiving precedence, we cover the bread so it does not "see" the Beracha recited over the wine.
The question arises as to whether this applies on Mosa’eh Shabbat, as well. If there is bread on the table when a person recites Habdala, must he cover the bread? Here, too, he is reciting the Beracha over wine, which could "embarrass" the bread, and it would thus appear that the bread must be covered for Habdala just as it must be covered for Kiddush.
Indeed, the Shulhan Aruch rules (299:9; listen to audio recording for precise citation) that if one is eating a meal immediately after Habdala, he should either ensure that the bread is not on the table, or cover the bread on the table before reciting Habdala. Just as in the situation of Kiddush, the bread should be covered so it will not be "embarrassed" as a result of its being preceded by the wine.
The Mishna Berura (Rav Yisrael Meir Kagan of Radin, 1839-1933) comments that this applies only if one intends to eat right after Habdala. It sometimes happens that when one recites Habdala, there is bread on the table from Se’uda Shelishit, but he is not planning on sitting down to eat right after Habdala. In such a case, one does not have to cover the bread, because he will not be reciting a Beracha on it anyway, and there is thus no issue of "embarrassment." It is only when one recites Habdala with the intention of then sitting down to eat that he must cover the bread.
One situation where this can happen is when Tisha B’Ab falls on Sunday, in which case Habdala is recited on Sunday evening, before one breaks the fast. It is quite possible that the table will be set at the time of Habdala, and one must ensure in this case to cover the bread before reciting Habdala.
It should be noted that this applies to Mezonot food, as well. Like bread, Mezonot food that is on the table must be covered for Kiddush, and thus if one has on the table Mezonot food which he plans to eat immediately after Habdala, he must ensure to cover it for Habdala.
Summary: One who has bread or Mezonot food on the table during Habdala, and he plans to eat immediately after Habdala, must ensure to cover it during Habdala, just as bread and Mezonot food must be covered during Kiddush.