The eye socket or sealed beam mount is indented on each side for corresponding protrusions on the back of the bulbs. Unless he bulb is in the right place, protrusions in indents, the bulb will not sit down correctly within the holder.
This looks like there's no provision for the locating indents and so the bulbs are not fully down inside the socket.
Or..What holds the bulbs in the socket? In the stock configuration there's the stainless ring held by three small screws which goes onto the bulb and connects by the screws to the sockets. In your photo, georgiafj40, it looks like the bulb is sitting outside the ring. Is that why they appear to protrude?
The unit is held by the headlight ring, which is held down by 3 screws just as you describe. I'll post up a photo and it should become clear.