On the 2016 MacBook Pro, monospaced fonts are not lining up. It happens to just some buffers and can only be fixed by changing the default font size then changing it back. My font setting is:
'(default ((t (:family "Ubuntu Mono" :foundry "nil" :slant normal :weight normal :height 181 :width normal)))))
I have the exact same Emacs configuration on two other Macs and never experience this problem.