From Dot Derivative Discrepancy, I have tried the using \hspace{0pt} and
\makeatletter
\renewcommand{\dddot}[1]{%
{\mathop{\kern\z@#1}\limits^{\vbox to-1.4\ex@{\kern-\tw@\ex@
\hbox{\normalfont ...}\vss}}}}
\renewcommand{\ddddot}[1]{%
{\mathop{\kern\z@#1}\limits^{\vbox to-1.4\ex@{\kern-\tw@\ex@
\hbox{\normalfont....}\vss}}}}
\makeatother
after loading mathtools but the problem still persists.

\documentclass{article}
\usepackage{mathtools}
\begin{document}
\[
\dot{\mathbf{r}}\times\ddot{\mathbf{r}}\times\dddot{\mathbf{r}}
\]
\end{document}
In the case the font scheme I am using has any affect as well, the fonts are:
\usepackage[utf8]{inputenx}
\renewcommand{\rmdefault}{ppl}
\linespread{1.05}
\usepackage[scaled]{helvet}
\usepackage{courier}
\usepackage{eulervm}
\normalfont
\usepackage[T1]{fontenc}
\usepackage{textcomp}




\dotand\ddotis completely different from\dddotand\ddddot. You might be interested in redefining\dotand\ddotto be similar to\dddotand\ddddot. – Werner Sep 04 '13 at 18:00\dotand\ddotcome directly from a font; the triple and quadruple dots are cobbled together from pieces, so it's not surprising that they behave differently. the best solution, of course, would be for triple and quadruple dots to be in a font, as they should be in a full unicode font. – barbara beeton Sep 04 '13 at 18:18