Arya being a Master Assassin or not, isn't even the issue, in my opinion.
I'm willing to accept that she's become a godly ninja, since they've been beating us over the head with it, over the last 2 seasons, but what i take issue with, is the way they decided to implement these skills, just wasn't clever on any level.
She literally jumped out of off screen, going past dozens of people with no explanation.
Regardless of how "realistic" that is, it's just not fun from a storytelling perspective, because it doesn't respect its own rules, it's just a cheap editing trick, that betrays your suspension of disbelief as a viewer.
That's what a plot-hole really is, it's breaking the established rule-set, for convenience's sake.
I'm ok with Arya killing the NK using her ninja skills, but come up with some fucking method she actually implements, that isn't abusing the editing software to teleport behind him, just because you're too lazy to write yourself out of that corner.