I suspect this is a bug
\documentclass{article}
\usepackage{tikz}
\usetikzlibrary{circuits}
\begin{document}
\begin{tikzpicture}[circuit]
\draw (0,0) to [circuit handle symbol={draw,shape=rectangle,at start}] (0,3);
\draw (1,3) to [circuit handle symbol={draw,shape=rectangle,at end}] (1,0);
\end{tikzpicture}
\end{document}
Compiled with expected output before upgrading pgf. The two lines ending in a small rectangle should be identical. In the case of at end it seems that the rectangle is rotated and thus moving the paths end point from the expected end point.
See https://github.com/pgf-tikz/pgf/issues/412