In this MWE the first  a is shifted to the left of the stem but the second one 
isn't. OK, it's a bit cramped, but I thought that the noteheads were scaled to 
the size of the staff to avoid this. 
Oddly, if the local staff size is changed to a global staff size, the anomaly 
\version "2.19.52"

\language "english"
{ \new Staff { 
  <c'' e'' a''>4 <c' e' a'>  

\layout {
  #(layout-set-staff-size 14) 



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