I can run the following code without any issue in TeXstudio with the Tex Live distribution.
\documentclass{article}
\usepackage[utf8]{inputenc}
\usepackage[european]{circuitikz}
\usepackage{tikz}
\usetikzlibrary{shapes, calc, intersections}
\usepackage{pgfplots}
\pgfplotsset{compat=1.14}
\usetikzlibrary{pgfplots.groupplots}
\usepackage{siunitx}
\usepackage{amsmath}
\usepackage{amssymb}
\usepackage{amsfonts}
\usepackage{subcaption}
\renewcommand*{\j}{\mathrm{j}}
\begin{document}
\begin{figure}[h]
\begin{tikzpicture}[trim axis right, remember picture]
\begin{semilogxaxis}[
name=mag,
width=\linewidth,
height=0.5\linewidth,
ylabel=$20\log_{10}\left(|H\!(\j2\pi f)\right|)$,
%xlabel=$f\,/\,\si{\Hz}$,
xmin=1000, xmax=1e10,
grid=both, minor grid style=dotted, minor y tick num = 4,
xticklabels={}]
\addplot [thick, name path=mag] table[x=Magnitude X, y=Magnitude Y, col sep=comma] {bode.csv};
\draw[red, thick, name path=0dB] (axis cs:1e3,0) -- (axis cs:1e10,0);
\path [name intersections={of=mag and 0dB,by={intmag}}] (intmag) \pgfextra{\pgfplotspointgetcoordinates{\pgfpointanchor{intmag}{center}} \xdef\myx{\pgfkeysvalueof{/data point/x}}\typeout{\myx}};
\end{semilogxaxis}
\begin{semilogxaxis}[
name=phase,
at={($(mag.south) - (0,0.05\linewidth)$)},
anchor=north,
width=\linewidth,
height=0.5\linewidth,
xmin=1000, xmax=1e10,
xlabel=$f\,/\,\si{\Hz}$,
ylabel=$\arg\{H(\j2\pi\omega)\}$,
grid=both, minor grid style=dotted, minor y tick num = 4]
\addplot [thick, name path= phase] table[x=Phase X, y=Phase Y, col sep=comma] {bode.csv};
\draw[red, thick, name path= PM] (axis cs:1e3,0) -- (axis cs: 1e10,0) coordinate (pmend);
\end{semilogxaxis}
\path [draw, name intersections={of=mag and 0dB,by={intmag}}, name path=vertical] (intmag) coordinate (IM) -- (IM|-phase.south);
\draw [latex-latex, name intersections={of=vertical and PM, by={intpm}}] (intpm) -- (intpm|-pmend) node[midway, left] {$PM$};
\end{tikzpicture}
\caption{Closed-loop Bode plot without Miller compensation}
\end{figure}
\end{document}
But if I try to run it on Overleaf it fails. This is the output log. bode.csv can be found here
circuitikzandpgfon OL servers is still too old to support your code. Sorry about this! – imnothere Dec 19 '18 at 02:12pgfplotsversion? I believe it was released in April – jagjordi Dec 19 '18 at 13:08