Do you have provisions for a queen excluder

A. With the Top Bar hive you don't need a Queen Excluder. You could use one but it would slow down production because the bees have to get through the small exclusion holes. I have only had one hive that extended the brood into the honey stores.

There are techniques that Top Bar beekeepers use to keep the brood separate from the honey stores. The first being, when you first put the bees into the hive, you use the "false back" included with the Backyard Hive and locate it 2/3 from the back of the hive. This procedure lets the bees set up home in the front of the hive. After a about 3-5days  when the bees have establlished building combs, you can move the false back to the rear of the hive. Then bees will tend to keep the brood in the front where they have drawn out their first combs which the queen will quickly start laying eggs in and then they extend the honey reserves out toward the back of the hive.

If the bees have a tendency to extend the brood too far you can remove a comb near the back of the brood combs and replace it with an empty top bar. This breaks up the continuous run of brood and the queen rarely ventures across this threshold. It is more natural for the queen to keep the brood close together then not. In some circumstances a particular strain of bees has forgotten this strategy.

The problem I have seen more is the bees mixing pollen stores amidst the honey stores. I have found this to be mainly due to the genetics/behavior of the bee colony. The pollen should be cut out of the honeycombs so it doesn't cloud and ruin the honey you process. You can "shell" the pollen out of the comb and store it in the refrigerator and can be eaten. Start with a small amount, one cells worth until your body gets use to it. The pollen has many beneficial properties and is a great source of protein.

The same strategy as the queen exclusion can be used for the pollen being put into the honey combs. Move the pollen combs toward the brood and leave an empty bar between the pollen dominant comb and the honey combs.