The boundaries of structures like witch huts, nether fortresses, mineshafts, desert/jungle temples and strongholds don't get saved with the world file.

That's an issue because Minecraft keeps getting updates which sometimes might change the shape or the position of the structures.
When ever that happens mobs which only spawn inside the structures won't spawn there anymore.

The last time we saw that happening was the change of nether fortresses in 1.6.
By adding the chests to it the the random object which is used for generation was changed which caused the fortresses to generate in a different shape.
Therefor wither skeletons and blazes don't spawn in old fortresses anymore.
This post is covering this issue: https://mojang.atlassian.net/browse/MC-15547

Since the structures aren't saved it's impossible to fix the nether fortress issue. Either the old or the new fortresses will be broken.

I decided to post this issue even though the nether fortress issue is related to the same cause because I want to suggest that the mistake isn't made again for neither for nether fortresses nor for other structures.

The other structures should be mentioned in this context since 1.7 is a biome update and changes to the structures are not unlikely.