Yeah, I can't imagine Ford messing up on the eye color, either. Ben Barnes (and Logan) definitely has brown eyes.
The only thing that has ever really made me question Logan vs William as MiB was the line MiB delivers to Teddy: "You used to be beautiful. When this place started, I opened one of you up once. A million little perfect pieces." And then we saw Logan do that very thing in ep9. But would it be that unusual to do that in this world? I know I would be curious about what was in there.