Hostile Mobs will not spawn at certain heights if the darkness they would spawn in is caused by the night. So if the skylight is 0 mobs WILL spawn at these heights.

The heights are:
16, 32, 48, 64, 80, 96, 112, 128, 144, 160, 176, 192, 208, 224, 240
(basicly every 16*n)

I guess this is due to the fact that Chunks are split up vertically in parts with the height of 16. So the problem occurs if a mob spawns inside one part, but the block it spawns on is inside the part below.

How to reproduce:

1. Singleplayer
2. Create new World
3. Gamemode: Creative
4. More World Options...
5. World Type: Superflat
6. Customize
7. Presets
8. paste the following preset into the box at the top: 3;64*minecraft:stone;1;
9. Use Preset
10. Done
11. Create new World
12. set the time to night (/time set 18000)

No mobs will spawn!
You can use the preset 3;63*minecraft:stone;1; or 3;65*minecraft:stone;1; instead and they will spawn.