Curious. I have just repeated your setup. In my Workbench HD. I selected the R-Billy G-Brand body and the images of its 2 pickups appear in the neck and bridge positions with both pickups active. When I select the Middle pickup its image appears in the middle position. However, the bridge pickup is deactivated and its image becomes translucent. In effect the guitar remains a 2-pickup guitar with the bridge pickup active and moved to the middle position even though its translucent image remains. When I deselect the Middle pickup its image disappears and the bridge pickup image remains translucent. It can be reactivated by selecting the Bridge pickup.
I experimented a bit. The behaviour changes depending on which of the Neck and Bridge pickups (or both) are active/selected when you select the Middle pickup. However, at all times, the image shows only one or two pickups active. You can't have no active pickups, and you can't have three active on that body type. You can, however, arrange to have only the middle pickup active. In that case you can't delete it because you would then have no active pickups. As mentioned, there must be one or two pickups active and selected at all times.
From your picture it appears you may have swapped (clicked/dragged) the positions of the pickup images at some point. By doing so I did manage to create the situation shown in your picture: three pickup images are present with the neck and bridge pickups active while the middle pickup image is translucent and can't be removed because Workbench HD knows it is one of the original two pickups.
I don't think it's a bug but it is confusing.