Sorry bro, it's just shitty judging.
http://fightmetric.com/fights/Machida-Shogun.html
Shogun landed 82 strikes out of 149.
Lyoto landed 42 strikes out of 116.
Shogun had 55% accuracy
Lyoto had 36% accuracy
Shogun landed 17 shots to the head (12 power shots).
Lyoto landed 14 shots to the head (8 power shots).
Lyoto landed 24 shots to the body
Shogun landed 16 shots to the body
Shogun landed 49 leg kicks.
Lyoto landed 4 leg kicks.
Shogun landed 48 strikes from distance.
Lyoto landed 26 strikes from distance.
Shogun landed 34 strikes from the clinch.
Lyoto landed 16 strikes from the clinch.