GraphViz
I would have also suggested to use the compass functionality of graphviz by adding :w to the edges:
digraph {
graph [rankdir = LR]
node [shape=box]
X1;X2;a[label="X1*X2"];Y
{X1,X2,a}->Y[arrowsize=0.5]
X1:w->X2:w[constraint=false dir=both arrowsize=0.5]
X2:w->a:w[constraint=false dir=both arrowsize=0.5]
a:w->X1:w[constraint=false dir=both arrowsize=0.5]
}

However, graphviz does not provide a possibility to adjust the default port locations for dot - graphviz version 2.40.1 (20161225.0304) (afaik). And in your case I think this is what you want to do.
yEd
The free, but not open-source, gui tool yEd supports this:

PSTricks & pst-node
If you do not mind to use something from the LaTeX world, here is a solution using pstricks and the package pst-node:
% ! TEX program = pdflatex -shell-escape
\documentclass{standalone}
\usepackage{pstricks-add}
\usepackage{auto-pst-pdf}
\usepackage{pst-node}
\begin{document}
\begin{pspicture}
\psset{linewidth=.3pt}
\rput(0,3){\rnode{A}{\psframebox{\makebox[1.1cm]{$X_1$}}}}
\rput(0,2){\rnode{B}{\psframebox{\makebox[1.1cm]{$X_2$}}}}
\rput(0,1){\rnode{C}{\psframebox{\makebox[1.1cm]{$X_1*X_2$}}}}
\rput(2,2){\rnode{D}{\psframebox{\makebox[1.1cm]{$Y$}}}}
\psset{angleA=0, angleB=180, arm=0}
\ncdiag[offsetB=+3pt]{->}{A}{D}
\ncdiag[offsetB=+0pt]{->}{B}{D}
\ncdiag[offsetB=-3pt]{->}{C}{D}
\psset{offset=3pt, angle=180, linearc=.25, armB=12pt}
\ncangle{<->}{A}{B}
\ncangle{<->}{B}{C}
\ncangle[linearc=.3333, armB=18pt]{<->}{C}{A}
\end{pspicture}
\end{document}
Compiling this document to pdf with $ pdflatex -shell-escape <filename> gives you

Finally, a tikz solution
\documentclass[tikz]{standalone}
\tikzset{>=stealth} % nicer default arrow tip
\begin{document}
\begin{tikzpicture}[every node/.style={rectangle,draw,minimum width=1.5cm}]
\node (a) at (0,2) {$X_1$};
\node (b) at (0,1) {$X_2$};
\node (c) at (0,0) {$X_1*X_2$};
\node (d) at (2.5,1) {$Y$};
\tikzset{every edge/.append style={->}}
\path (a.east) edge ([yshift=+3pt]d.west);
\path (b.east) edge ([yshift=+0pt]d.west);
\path (c.east) edge ([yshift=-3pt]d.west);
\tikzset{out=-180,in=180,every edge/.append style={<->,looseness=1.5}}
\path ([yshift=-3pt]a.west) edge ([yshift=+3pt]b.west);
\path ([yshift=-3pt]b.west) edge ([yshift=+3pt]c.west);
\path ([yshift=+3pt]a.west) edge ([yshift=-3pt]c.west);
\end{tikzpicture}
\end{document}
