I need a table of contents at the beginning of my appendix section. However, the following includes sections from the main text as well

\appendix
\tableofcontents


How can I get rid of those sections from the main text and just keep the ones from the appendix?

Background: It is quite logical that the table of contents is just created for the entire file, since every chapter/section/subsection/etc. are written to a .toc file and the \tableofcontents command just reads from that file (this is also thereason why you have to compile twice in order for the toc to be included correctly.

Now, to solve your question, you can use the minitoc package like this:

\documentclass[a4paper]{article}
\usepackage{minitoc}

% Make the "Part I" text invisible
\renewcommand \thepart{}
\renewcommand \partname{}

\begin{document}
\doparttoc % Tell to minitoc to generate a toc for the parts
\faketableofcontents % Run a fake tableofcontents command for the partocs

\part{} % Start the document part
\parttoc % Insert the document TOC

\section{First}
First content.
\section{Second}
Second content.

\newpage
\appendix