Runegraft overrides do not allow you to assign the mastery it overwrote elsewhere.

I'm not sure if this is intended. The mastery is supposed to be a throwaway so you can just throw on a runegraft on it, but overriding it with a runegraft doesn't allow you to take said mastery on another node.

I can confirm this bug.
I had the life mastery which gives 15% more life if your body armour does not have life on it. I overwrote it with a runegraft of treachery. I wanted to select the mastery on a different node but it keeps saying that I already have the mastery selected.

U can still respec it at Faustus and swap it out, no problem