I had this issue when playing hardcore minecraft a month or two ago and it seems to have been forgotten, or ignored. When creating a villager holding pen, if there is a two block space directly beneath the villagers, zombies will spawn at night, sometimes right beside where you are standing. The entire area is surrounded by fences and cactus, as well as being more than adequately torch lit. There is obviously something wrong with zombie spawning behavior.

The zombies spawn here, directly under where my villagers are stored. Here is a link to a download of this current world, as well.