Neither the encroachment nor Livakovic standing 3mm off the line resulted in any advantage. Kane got a free, unimpeded shot and he missed. You can't just recall things a technicality, the game would be unplayable.
Rules should only be enforced if the breach resulted in a clear advantage. You can't recall every kick just because players were standing 3mm in the wrong area. The whole game would be unplayable then. It's impossible for goalkeepers to stand exactly on the line while diving.