Delete package 'subfig', and use package 'subcaption'
Delete the 'subcaption' package and add:
\usepackage[caption=false,labelformat=simple]{subfig}
\renewcommand\thesubfigure{(\alph{subfigure})}
(1) Open the command panel on VS code (Ctrl+Shift+P for Windows and Cmd+Shift+P for Mac). (2) Search for Kill VS Code Server on Host, click it - it will be automatically deleted. (3) Reload VS Code and establish the connection again.
natbib automatically loads achemso package, so change the command: \bibliographystyle{achemso}
The order of loading these two packages matters. Should first load markdown and then load enumitem. The reason MIGHT BE the markdown package redefines the enumerate and itemize environment, thus incurring a conflict.
Use \PassOptionsToPackage{prologue,dvipsnames}{xcolor} before \documentclass, and then add \usepackage[dvipsnames]{xcolor}.
\let\Bbbk\relax \usepackage{markdown}
\setcounter{figure}{2}
\setcounter{subfigure}{0}
\begin{subfigure}
\setcounter{figure}{2}
\setcounter{subfigure}{0}
\centering
\begin{minipage}[b]{0.5\textwidth}
\includegraphics[width=\linewidth]{logo1.eps}
\caption{This is Subfigure 1.}
\label{fig:Subfigure 1}
\end{minipage}
\setcounter{figure}{2}
\setcounter{subfigure}{1}
\begin{minipage}[b]{0.5\textwidth}
\includegraphics[width=\linewidth]{logo2.eps}
\caption{This is Subfigure 2.}
\label{fig:Subfigure 2}
\end{minipage}
\setcounter{figure}{2}
\setcounter{subfigure}{-1}
\caption{Enter the caption for your subfigure here. \textbf{(A)} This is the caption for Subfigure 1. \textbf{(B)} This is the caption for Subfigure 2.}
\label{fig: subfigures}
\end{subfigure}