Rust removal ended with black oxide on the metal? I have tried to remove common red iron rust from a small piece of metal that looks like steel. 

I submerged it into hot water with a bit of citric acid, and let it sit overnight. In the morning I have no rust, but the thing is now covered in dark-black oxide.

Was that possibly steel that I was cleaning or something else? How do I remove that black oxide?  

How should remove rust in situations like this in the future?!

left - piece from the same metal that has no rust, and was not cleaned, right - piece that was cleaned
In the absence of oxygen iron reacts with water forming $\ce{Fe(OH)_2}$, which can react with rust forming $\ce{Fe_3O_4}$ via the Schikorr reaction.  See https://en.m.wikipedia.org/wiki/Schikorr_reaction.

You should use a stronger acid, which will dissolve the rust and bring the iron ions into solution.  You will, of course, lose the original metal that rusted instead of recovering it, but you can't make such a recovery by "home remedies" anyway.  With such an aggressive approach rethink soaking overnight.