Holmes offers a logical explanation for almost everything, but there are points where there's either no explanation or the logic is sound but might not be accurate.
Second? Blackwood surviving. Yes, Holmes offers a theory, but we have no concrete evidence in the movie. There is no glimpse of the harness except in the flashback, which is Holmes!logic.
Third? Standish and his gun. We have no idea when the bullet could have been substituted OR how Blackwood could be sure Standish wouldn't try and use his gun until that moment.
Four? The prison guard. Holmes suggests Blackwood paid him to act possessed, and this is very possible, but we have no proof either way. Combined with point 1, I admit to wondering.