From my stand point i don't think thats a bug. The console while useful for fixing mistakes and mishaps that in game bugs do, is mostly used to cheat ie spawn urself a nice gun or some ammo, npcs, and even kill npcs ( as i remember u could do in Oblivion). How is it an achievement if you cheat? Or am i missing your point of view?
It's definitely intended. As far as I know if you use the console you have to save, exit out of the game and come back in to enable the achievements again. I haven't tried but you may have to do that if you just open the console, i.e. accidentally press the ~ key. You can disable the ~ key in one of the .ini files. As always, make a copy of the .ini file before editing it.