Duplicated Prefabs not behaving as expected

Hi everyone.

Been having this really frustrating problem that is slowing down my work quite considerably. Couldn't find anything else related to it on the forums.

I'm building a level out of prefab blocks (wall sections, floor sections). The fastest way is to use Ctrl+D to duplicate the prefab in the scene. The problem is that when I duplicate the prefab, unless I press "Apply" on the newly duplicated object, it acts as if it's not part of the prefab.

So if i modify the prefab, none of these duplicates are modified along with it. Is this a bug or is there something i'm missing? Perhaps some annoying feature?

It's too frustrating to work this way. There must be a better solution.

Thanks in advance!