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I created a figure with four subfigures (two rows of two subfigures) where each subfigure has a caption below the subfigure. Strangely, the captions for the subfigures in the top row are partially covered by the subfigures in the second row. I can't seem to figure out why that is or how to fix it. An example of the code is given below.

\subfigure[$k$~$=$~0.5]{\label{fig:2}\includegraphics[scale=0.4]{Fig2}} \\
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It seems that the borders of the figures itself are not correct. An easy way to check this is to surround each one with a \fbox, e.g. replacing \includegraphics[scale=0.4]{Fig1} with \fbox{\includegraphics[scale=0.4]{Fig1}}.

(Something different: I recommend using \centering instead of \begin{center}...\end{center} because the latter one will produce unwanted vertical space between figure contents and caption.)

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