I will try to explain this as best as possible. Please forgive me if this is confusing.

Placing doors for a village quits adding any doors to the village if any doors are placed above (3 block distance as shown in the pictures).

The doors on the upper area are not registering in NBTExplorer as doors for the village even though they are valid doors (built the same way as the ones on the bottom.

The doors seem to stop adding after two blocks going up.

Please let me know if you need any more information

EDIT: I first noticed the issue in my multiplayer server after adding more doors to an Iron Golem farm and not having the villagers breed (the conditions were correct). I checked the villages.dat file and none of the doors that i had added (they were all above the initial doors added) registered as added in the file. I could add and remove doors on the initial layer perfectly fine though. The screenshot was taken in a brand new world created in single player and I did some testing and was able to replicate the same behavior for the doors.