Q:

Wrong numbering in the List of Figures with subfigure package

I get a wrong numbering of subfigures in the List of Figures with the following MWE.
If I remove the FIGTOPCAP option or if I put the \caption on the top, the problem is solved, but I'd like keep them. Any idea?
\documentclass{book}
\usepackage[tight,FIGTOPCAP]{subfigure}
\setcounter{lofdepth}{2}

\begin{document}
\listoffigures

\begin{figure}
    \frame{
        \begin{minipage}[t]{0.4\textwidth}
            PIC 1
        \end{minipage}
    }
    \caption[Short Caption]{Long Caption}
\end{figure}

\begin{figure}
    \subfigure[Sub-caption A]{\label{LabelA}%
        \frame{
            \begin{minipage}[t]{0.4\textwidth}
                PIC 2A
            \end{minipage}
        }%
    }
    \hfill
    \subfigure[Sub-caption B]{\label{labelB}%
        \frame{
            \begin{minipage}[t]{0.4\textwidth}
                PIC 2B
            \end{minipage}
        }%
    }%
    \caption[General Short Caption]{General Long Caption\label{GenLabel}}
\end{figure}
\end{document}

A:

The subfigure package has long be declared obsolete. You get correct output with the successor package subfig (notice that you must use \subfloat instead of \subfigure and \subtable); the \captionsetup is drawn from the documentation to emulate the old options.
\documentclass{book}

\usepackage{subfig}
\captionsetup[subfloat]{position=top,
  farskip=10pt,topadjust=0pt,captionskip=10pt,
  nearskip=10pt,margin=10pt}

\setcounter{lofdepth}{2}

\begin{document}
\listoffigures

\begin{figure}
\framebox[0.4\textwidth]{PIC 1}
\caption[Short Caption]{Long Caption}
\end{figure}

\begin{figure}
\subfloat[Sub-caption A]{\label{LabelA}%
  \framebox[0.4\textwidth]{PIC 2A}%
}%
\hfill
\subfloat[Sub-caption B]{\label{labelB}%
  \framebox[0.4\textwidth]{PIC 2A}%
}

\caption[General Short Caption]{General Long Caption\label{GenLabel}}
\end{figure}
\end{document}

Here is the "List of figures"

and here's the part with the subfloats

A:

The options FIGTOPCAP (and FIGBOTCAP) controls the settings for the normal caption as well as the subfigure’s caption. In your example, the subfigure’s caption were allocated to the first figure because they appeared after the first and before the second \caption.
The subfigure package offers three so called “flags” (→ subfigure manual, 4.5 “Aligning Captions Above the Figure”, pp. 23f.):

\subfiguretopcaptrue
\subfiguretopcapfalse
\figuretopcaptrue

Admittedly, I can’t fully follow the explanations and examples from the manual; the solution is to drop the FIGTOPCAP option and use \subfiguretopcaptrue (preferably in the preamble), as it does exactly what it says on the tin.
Code
\documentclass{book}
\usepackage[tight]{subfigure}
\subfiguretopcaptrue
\setcounter{lofdepth}{2}

\begin{document}
\listoffigures

\begin{figure}
    \frame{
        \begin{minipage}[t]{0.4\textwidth}
            PIC 1
        \end{minipage}
    }
    \caption[Short Caption]{Long Caption}
\end{figure}

\begin{figure}
    \subfigure[Sub-caption A]{\label{LabelA}%
        \frame{
            \begin{minipage}[t]{0.4\textwidth}
                PIC 2A
            \end{minipage}
        }%
    }
    \hfill
    \subfigure[Sub-caption B]{\label{labelB}%
        \frame{
            \begin{minipage}[t]{0.4\textwidth}
                PIC 2B
            \end{minipage}
        }%
    }%
    \caption[General Short Caption]{General Long Caption\label{GenLabel}}
\end{figure}
\end{document}

Output

