When I use a custom label in the enumerate environment, as follows:
\documentclass{amsart}
\newtheorem{theorem}{Theorem}[section]
\usepackage{enumitem}
\begin{document}
\begin{theorem}Consider the following conditions
\begin{enumerate}
\item[(xy)] Condition 1 \label{a:cond:1}
\item[($\neg$)] Condition 2 \label{a:cond:2}
\item[($\sim$)] Condition 3 \label{a:cond:3}
\end{enumerate}
\end{theorem}
I want \verb|\eqref{a:cond:2}| to output ``($\neg$)'' instead of
\eqref{a:cond:2}
\end{document}
The \label commands after each \item are assigning the label to the Theorem instead, so the output is not what I want it to be: 
Without the manually modified item labels, the output is as expected:
\documentclass{amsart}
\newtheorem{theorem}{Theorem}[section]
\usepackage{enumitem}
\begin{document}
\begin{theorem}Consider the following conditions
\begin{enumerate}
\item Condition 1 \label{b:cond:1}
\item Condition 2 \label{b:cond:2}
\item Condition 3 \label{b:cond:3}
\end{enumerate}
\end{theorem}
\verb|\eqref{b:cond:2}| works correctly: \eqref{b:cond:2} \eqref{a:cond:2}
\end{document}

Why is this behaviour occuring and how can I prevent it?

\@currentlabelset by\refstepcounter. See also https://tex.stackexchange.com/questions/236626/refer-to-the-name-of-an-equation-while-a-list-of-equations-is-generated-using/237126?s=1|2.0698#237126. – John Kormylo Sep 25 '17 at 04:25