My understanding is that, when placing a part, it will only attach to the one part you place it on. So you can place C on top of B on top of A, but you can't stick B in the middle of A and C and expect all three to be connected.
The bottom half of your assembly is attached to the top of the assembly only through that one Dart. It would appear from your comments that the other two Darts are attached to the bottom half. So while they may be touching the engine plate they are not connected to it. To fix this, you would need to pick up those Darts and place them on the engine plate by hand. Then they would be connected to the engine plate but not to the stack separators, or not to the three-way adapter.
That is, assuming it's not a bug.
