In a joint file, my picture was changed by some un-used global tikzstyle, which is added by other. Here is a minimal example. The output dots become bigger if I un-comment the commented line.
\documentclass{standalone}
\usepackage{tikz}
\usetikzlibrary{matrix,arrows,calc}
%\tikzset{cd/.style=matrix of math nodes,row sep=2em,column sep=2em, text height=1.5ex, text depth=0.5ex}
\begin{document}
\begin{tikzpicture}[mydot/.style={draw,circle,inner sep=1.5pt},every label/.style={scale=0.6},scale=0.75]
\node[mydot] at (0,0) (p1) {};
\node[mydot] at (2,0) (p2) {};
\end{tikzpicture}
\end{document}
