Stackengine centering problem

I think you are just not taking account of sidebearings of the characters so the actual character widths used for centering include some white space. TeX has no information about the glyph shape, it can not tell what parts of a specified character width are black.

\documentclass{article}
\usepackage{stackengine}
\begin{document}

$\left|\Shortstack[c]{Cognicion abstractiva}\right|$


$\left|\Shortstack[c]{\frame{Cognicion} \frame{abstractiva}}\right|$
\end{document}

This example should lift any doubt about what to measure; note that in the first two cases the hairlines are perfectly superimposed to each other, showing that there's no issue with \Shortstack.

On the other hand, the difference you measured is less than 0.4pt, too small to be really noticeable: it depends on the bounding boxes of the characters.

\documentclass{article}
\usepackage{color}
\usepackage{stackengine}
\newcommand{\hairline}[1][black]{%
  \leavevmode\kern-0.05pt
  \smash{\color{#1}\vrule height 20pt depth 20pt width 0.1pt}%
  \kern-0.05pt
}
\begin{document}
\centering
\Shortstack[c]{\hairline{}XXXXXX\hairline{} XXXXXXXXXX}

\hairline{}XXXXXX\hairline{}\\ XXXXXXXXXX

\vspace{20pt}

\Shortstack[c]{%
  \hairline[red]Cognicion\hairline[red]
  \hairline[green]abstractiva\hairline[green]%
}
\end{document}