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It can take a while to get accustomed to shoot wide open with lenses f/1.4 or faster. Think for example that if you're doing a closeup and you focus, then re-compose, you maybe have moved your camera slightly changing the angle of the focal plane. For a razor-thin DOF in the case of f/1.4, you'll most likely have the focus somewhere else.
One good thing to do is focus and when recomposing try not to lean camera (and consequently the focal plane) forward, try to keep it in the same plane where it was when you framed it.

The best way to check whether is something wrong or not, is to have your camera on tripod, make some test shots at f/1.4 at various distances and use the microadjustment if necessary. If the focus point is way off when you shoot from tripod, then go back to nikon and tell them if they don't fix it you'll smash their front elements to bits.

In this case I would return the lenses if I were you. And because you're on Nikon, I think you'd be better off with the Sigma 50mm f/1.4 DG EX. Regarding bokeh cream is only second to Canon's f/1.2L. Sharp wide open, I have quite a few images shot at f/1.4 on SS and the other websites.
There's a Sigma 85mm f/1.4 too - not exactly as great as the Canon's 85 f/1.2L, but at least as good as Nikon f/1.4 (again, bokeh quality).
Anyway, very fast primes are prone to focus shifting, but that's when stopping down. And some of them can have focus problems wide open around the minimum focusing distance