Random numbering and spacing of sub-figures in pdf output

Question

The numbering of the sub-figures in my pdf output is kind of random, but in the editor the numbering is as it should be.

Where the sub-figures are correctly numbered from (a) to (d), but when exported to pdf, this is what i get:

I would also like to ask why is the horizontal spacing in the first row of figures different? The settings for each line are the same yet the first row does not follow.

I dont know how to fix this. Here is a LaTeX code of the figure:

%% LyX 2.3.2-2 created this file.  For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass[english]{IEEEtran}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\usepackage{graphicx}

\makeatletter
\@ifundefined{showcaptionsetup}{}{%
 \PassOptionsToPackage{caption=false}{subfig}}
\usepackage{subfig}
\makeatother

\usepackage{babel}
\begin{document}
\begin{figure*}
\subfloat[]{\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_0_ground_truth}}\enskip{}\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_1_ground_truth}}\enskip{}\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_2_ground_truth}}}

\subfloat[]{\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_0_ground_truth}}\enskip{}\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_1_ground_truth}}\enskip{}\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_2_ground_truth}}}

\subfloat[]{\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_0_ground_truth}}\enskip{}\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_1_ground_truth}}\enskip{}\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_2_ground_truth}}}

\subfloat[]{\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_0_ground_truth}}\enskip{}\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_1_ground_truth}}\enskip{}\subfloat{\includegraphics[width=0.28\paperwidth]{volume_4_2_ground_truth}}}

\caption{Comparison}
\end{figure*}

\end{document}

Answer 1

If I understood correctly that you need only four captions (from (a) to (d), one per row), you may simply remove the nested \subfloat:

\documentclass[english]{IEEEtran}
\usepackage[T1]{fontenc}
\usepackage[latin9]{inputenc}
\usepackage{graphicx}

\makeatletter
\@ifundefined{showcaptionsetup}{}{%
 \PassOptionsToPackage{caption=false}{subfig}}
\usepackage{subfig}
\makeatother

\usepackage{babel}
\begin{document}
\begin{figure*}
\centering
\subfloat[]{%
    \includegraphics[width=0.25\paperwidth]{example-image}\enskip
    \includegraphics[width=0.25\paperwidth]{example-image}\enskip
    \includegraphics[width=0.25\paperwidth]{example-image}%
}

\subfloat[]{%
    \includegraphics[width=0.25\paperwidth]{example-image}\enskip
    \includegraphics[width=0.25\paperwidth]{example-image}\enskip
    \includegraphics[width=0.25\paperwidth]{example-image}%
}

\subfloat[]{%
    \includegraphics[width=0.25\paperwidth]{example-image}\enskip
    \includegraphics[width=0.25\paperwidth]{example-image}\enskip
    \includegraphics[width=0.25\paperwidth]{example-image}%
}

\subfloat[]{%
    \includegraphics[width=0.25\paperwidth]{example-image}\enskip
    \includegraphics[width=0.25\paperwidth]{example-image}\enskip
    \includegraphics[width=0.25\paperwidth]{example-image}%
}

\caption{Comparison}
\end{figure*}

\end{document}

Answer 2

Use \includegraphics command inside minipages of your desired width.

\documentclass[english]{article}
\usepackage[T1]{fontenc}
\usepackage{graphicx}
\usepackage{subcaption}
\begin{document}

\begin{figure*}
\begin{minipage}{0.3\textwidth}
\includegraphics[width=\linewidth]{volume_4_0_ground_truth}
\end{minipage}\hspace*{\fill}
\begin{minipage}{0.3\textwidth}
\includegraphics[width=\linewidth]{volume_4_1_ground_truth}
\end{minipage}\hspace*{\fill}
\begin{minipage}{0.3\textwidth}
\includegraphics[width=\linewidth]{volume_4_2_ground_truth}
\end{minipage}\vspace{15pt}

\begin{minipage}{0.3\textwidth}
\includegraphics[width=\linewidth]{volume_4_0_ground_truth}
\end{minipage}\hspace*{\fill}
\begin{minipage}{0.3\textwidth}
\includegraphics[width=\linewidth]{volume_4_1_ground_truth}
\end{minipage}\hspace*{\fill}
\begin{minipage}{0.3\textwidth}
\includegraphics[width=\linewidth]{volume_4_2_ground_truth}
\end{minipage}
\caption{Comparison}
\end{figure*}

\end{document}

A caption can be included if you wish by using the command: \captionof{subfigure}{Caption (a)}