This happens because of the extra vertices and surfaces that dont disapear when you just merge two or more objects. To get that to work you have to remove the surfaces hidden between the objects and weld the vertices. To get that to work the two vertices have to be in the exact same place. In the picture you see two cubes. They are merged but when subdivided they becomme two objects. I then deleted the extra surfaces and welded the vertices. And then they act as they should.
But in your case I would have just extruded from the middle object instead. Much more easy, and you dont have to worry about the extra surfaces and vertices. Hope this helps
