I have 2 equations. When I use \ref{} for the second equation, it gives the correct number but directs to the wrong place. How can I fix this? Thanks

\documentclass[12pt]{article}
\usepackage{amsmath}
\numberwithin{equation}{subsection}
\usepackage{hyperref}
\begin{document}
\section{Chapter 16}
\subsection{16.2}
$$\int_{C}f(x,y)ds=\int_{a}^{b}f\left(x(t),y(t)\right)\cdot |\vec{r}\,'(t)|\cdot dt \label{2d}$$
\subsection{16.3}
See \ref{2d}
\subsection{16.6}
$$|\vec{r}_x\times \vec{r}_y|=\sqrt{1+\left(\dfrac{\partial f}{\partial x}\right)^2+\left(\dfrac{\partial f}{\partial y}\right)^2} \label{area}$$
\subsection{16.7}
See \ref{area}
\end{document}

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Did you run latex twice? – Sigur Jul 31 '14 at 1:17
Welcome to TeX.SX! – Adam Liter Jul 31 '14 at 1:18
Welcome! Please provide a minimal example to facilitate the debugging. Sigur suggestion should sort it out! – anderstood Jul 31 '14 at 2:55
Looking at the aux file, both labels refer to equation.16.1, ignoring the subsection number. Not sure how to fix it yet. – John Kormylo Jul 31 '14 at 3:34
It's not \theequation, and \subsection definitely calls \refstepcounter. – John Kormylo Jul 31 '14 at 4:21

Put your \numberwithin{equation}{subsection} line after \usepackage{hyperref}. Apparently there is a conflict between amsmath and hyperref.