I was playing on a survival multiplayer server where we have limited claim space. So I decided to stack the breeding stations about 10-15 blocks above each other. This however caused the pokemon within the ones below the top to not show up. They still would breed but you could not check the status of affection or even see them. They also did not fall off I checked all around I even took them out and respawned them. This has been a very difficult thing to deal with.

Anything placed above a ranch block interferes with the ranch checks, so all of your ranches are using whatever material you have as the top one