Fences and maybe other typ of placeable items are quite problematic when creating a blueprint. Once you have started the building process, hearthling will try to place the items and when you place them inside of each other (which is possible with fences), then the building will never be finished. The hearthlings will try to place the fences and if there is no room, they will place it as close a possible to the original position. But since the ghost of the item will not disappear in the blueprint, the building never counts as finished.
My workaround: Not placing any kind of furniture in blueprints, do this by manually by hand. Keep the buildings simple.
Summary:
I guess its not a bug, since tghe new fencetool is not implemented yet, but the result is still there.
I made a sheepfarm where i wanted to use the fences and a gate. In the designfase it all looked as intended, but when the building was completed the result was not as intended. Steps to reproduce:
Create a building with fences next to buildingblocks, so the interact.
Build the building
Notice the placement of the fences now cant interact with the buildingblocks.