Q. Is there a “bee parts” issue, (when eating a piece of a honeycomb), since I’ve been told that pieces of the bee itself remain in the honeycomb? ( It was bought in a COR hechshered store)

A. Unfiltered honey that has insect parts in it, has to be strained before consuming. Although bee parts are not kosher, bee legs are considered inedible “atzamos” or bones and are not Biblically prohibited. (Pri Chadash Y.D. 81:27, based on Tosfos Avoda Zara 69a – “Hahu”).  The Rosh (Avoda Zara 5:11) notes that bee legs and wings are “k’afar b’alma,” or similar to dust, and therefore not Biblically prohibited.
If prior to filtration the honey was heated (in a kosher equipment) with the parts inside, the honey would not become treif. (Shulchan Aruch Y.D. 81: 8). This is because the bee parts only impart a bad taste into the honey that after the fact do not compromise the kosher status of the honey (nosain ta’am lifgam).
Horav Shlomo Miller’s Shlit’a opinion is that you have to check for (if they are regularly there) and extract the insect parts if any that you can see, from the unfiltered honeycomb crushed before Shabbos. You can do so during Shabbos by using a spoon  and removing some of the honey with them.

Rabbi A. Bartfeld as revised by Horav Shlomo Miller Shlit”a