A recurring motif in last night's episode was that Holmes doesn't
Nothing about Bell's apartment told him that Bell had a brother.
Watson, not Holmes, sees the evidence that linked Reyes to the murder.
There's two. It's entirely plausible that Holmes missed the third -- that Watson was no longer being paid to be his sober companion -- because she continued to behave as though she were, giving him no reason to believe that she wasn't. Holmes is smart. Holmes is observant. But Holmes isn't infallible.