You have defined your subfigure environments to have a width of .3\textwidth, but your images are wider than that, so they will stick out on the right side. This is also the reason the captions are narrow, as they have the same width as the subfigures. So to fix this, just increase the width. You can use \columnwidth to make them as wide as the columns.
See the below code for an example, where I also added an \fbox around the each subfigure, so their boundaries are obvious.
\documentclass{article}
\usepackage{graphicx}
\usepackage{subcaption}
\begin{document}
\begin{figure}
\centering
% this is wide enough
\fbox{\begin{subfigure}[b]{\textwidth}
\centering
\includegraphics[width=7cm,clip=false]{example-image-a}
\caption{Some long caption some long caption some long caption}
\end{subfigure}}
% this has a too narrow subfigure
\fbox{\begin{subfigure}[b]{0.3\textwidth}
\includegraphics[width=7cm,clip=false]{example-image-b}
\caption{Some long caption some long caption some long caption}
\end{subfigure}}
\caption{Label predictions using cross-correlation-, GTW-, and LSTM-based classifiers}
\end{figure}
\end{document}
Here's a flexible solution; in a figure environment you define with \xsubfigure the objects you need and then arrange them as you like. Each command has as a first argument a symbolic key to be used in \makerow; the second argument defines the objects via a key-value syntax (add \label in the body of caption, if needed).
\documentclass{article}
\usepackage[font=footnotesize]{subcaption}
\usepackage[demo]{graphicx}
\usepackage{xparse}
\ExplSyntaxOn
\NewDocumentCommand{\xsubfigure}{ m m }
{% #1 is a symbolic key, #2 is a list of key-value pairs
\roly_xsubfigure:nn { #1 } { #2 }
}
\NewDocumentCommand{\makerow}{ m }
{% #1 is a list of symbolic keys
\roly_makerow:n { #1 }
}
% define the keys
\keys_define:nn { roly/subfigures }
{
width .tl_set:N = \l_roly_subfig_width_tl,
body .tl_set:N = \l_roly_subfig_body_tl,
caption .tl_set:N = \l_roly_subfig_caption_tl,
}
% the needed variables
\dim_new:N \l_roly_row_height_dim
\box_new:N \l_roly_body_box
% this is the inner command that stores the properties
\cs_new_protected:Npn \roly_xsubfigure:nn #1 #2
{
\prop_if_exist:cTF { l_roly_subfig_#1_prop }
{
\prop_clear:c { l_roly_subfig_#1_prop }
}
{
\prop_new:c { l_roly_subfig_#1_prop }
}
\keys_set:nn { roly/subfigures } { #2 }
\prop_put:cnV { l_roly_subfig_#1_prop } { width } \l_roly_subfig_width_tl
\prop_put:cnV { l_roly_subfig_#1_prop } { body } \l_roly_subfig_body_tl
\prop_put:cnV { l_roly_subfig_#1_prop } { caption } \l_roly_subfig_caption_tl
}
% this is the inner command for producing a row
\cs_new_protected:Npn \roly_makerow:n #1
{
% get the heights of the objects on a row
\dim_zero:N \l_roly_row_height_dim
\clist_map_inline:nn { #1 }
{
\hbox_set:Nn \l_roly_body_box
{
\prop_item:cn { l_roly_subfig_##1_prop } { body }
}
\dim_compare:nT { \box_ht:N \l_roly_body_box > \l_roly_row_height_dim }
{
\dim_set:Nn \l_roly_row_height_dim { \box_ht:N \l_roly_body_box }
}
}
% produce a line
\clist_map_inline:nn { #1 }
{
% a subfigure is set here
\begin{subfigure}[t]{ \prop_item:cn { l_roly_subfig_##1_prop } { width } }
\raggedright
\vspace{0pt} % for top alignment
% the body is set in a suitably dimensioned parbox
\parbox[t][\l_roly_row_height_dim]{\textwidth}{
\prop_item:cn { l_roly_subfig_##1_prop } { body }
}
% add the caption
\caption{ \prop_get:cn { l_roly_subfig_##1_prop } { caption } }
\end{subfigure}
\hspace{2em} % some space between the objects in a row
}
\unskip\\ % end up the row
}
\ExplSyntaxOff
\begin{document}
\begin{figure}
\captionsetup[subfigure]{justification=justified,singlelinecheck=false}
\centering
\xsubfigure{A}{
width=0.3\textwidth,
body={\includegraphics[width=3cm,height=2cm]{fig/workflow-S}},
caption={workflow $S$ and some text added to go to the next line}
}
\xsubfigure{B}{
width=0.5\textwidth,
body={\includegraphics[width=6cm,height=2.5cm]{fig/workflow-S-run}},
caption={run of $S$}
}
\xsubfigure{C}{
width=0.3\textwidth,
body={\includegraphics[width=2cm,height=1.5cm]{fig/workflow-S'}},
caption={workflow $S'$}
}
\xsubfigure{D}{
width=0.5\textwidth,
body={\includegraphics[width=4cm,height=1cm]{fig/workflow-S'-run}},
caption={run of $S'$}
}
\makerow{A,B}
\medskip
\makerow{C,D}
\caption{Here's a figure}
\end{figure}
\end{document}
Note that if you're not satisfied with the arrangement, you can rearrange the subfigures by saying, for instance,
\makerow{A,D}
\medskip
\makerow{C,B}
In the example I set height and width for every \includegraphics, as I don't have your images, but you can use the keys you prefer.
Best Answer
Add this line to your preamble,
That will affect all the subfigure captions. For details (and other options), please keep reading on.
As is pointed out in the caption package documentation,
Now since you want only the subfigure captions to be left justified, you need to use the
\captionsetup[FLOAT_TYPE]{OPTIONS}command.FLOAT_TYPEcan be table,figure,subtableandsubfigureand specifies what type of caption that particular\captionsetupcommand applies to. So you can set different options for each of thefigure,table,subfigureandsubtablefloats individually.In your case the
FLOAT_TYPEwill besubfigure. If you put that\captionsetupcommand in the preamble, all your subfigure captions will be left justified. If you put that at some midpoint, all subsequent ones will get that effect. Should you need that for only one figure, put that inside that particularfigureenvironment.Here is the output.