Table in IEEE paper format

You should use the S columns of siunitx.

 documentclass[conference]{IEEEtran}
 IEEEoverridecommandlockouts

 usepackage{booktabs,tabulary,lipsum}
 usepackage{dcolumn,tipa}
 newcolumntype{d}{D{.}{.}{6.5}}
 usepackage{siunitx}
 usepackage[usestackEOL]{stackengine}
 usepackage{multirow}


 begin{document}

 begin{table*}[ht]
 sisetup{
 table-number-alignment = center,
 table-figures-integer = 1,
 table-figures-decimal = 4
 }
 caption{Table ex.}
 label{tab1}
 centering
 renewcommandfootnoterule{kern -1ex}
 renewcommand{arraystretch}{1.3}
 begin{tabular}{l*{8}{S}}
 toprule multirow{3}{*}{Subjects}   & 
 multicolumn{4}{c}{Numbers} & 
 multicolumn{4}{c}{Numbers}
 cmidrule(r){2-5}cmidrule(l){6-9}  &
 multicolumn{1}{c}{XYZ} & 
 multicolumn{1}{c}addstackgap{stackanchor{XYZ}{(Numbers)}} & 
 multicolumn{1}{c}{Numbers Tree} & 
 multicolumn{1}{c}{Numbers Tree} & 
 multicolumn{1}{c}{XYZ} & 
 multicolumn{1}{c}addstackgap{stackanchor{XYZ}{(Numbers)}} & 
 multicolumn{1}{c}{Numbers Tree} & 
 multicolumn{1}{c}{Numbers Tree} midrule 
 X1 & 0.5000 & 0.4888 & 0.0112 & 0.0001 & 0.8500 & 0.3540 & 0.2332 & 0.2367 
 X2 & 0.5000 & 0.4888 & 0.0112 & 0.0001 & 0.8500 & 0.3540 & 0.2332 & 0.2367  
 X3 & 0.5000 & 0.4888 & 0.0112 & 0.0001 & 0.8500 & 0.3540 & 0.2332 & 0.2367  
 X4 & 0.5000 & 0.4888 & 0.0112 & 0.0001 & 0.8500 & 0.3540 & 0.2332 & 0.2367  
 X5 & 0.5000 & 0.4888 & 0.0112 & 0.0001 & 0.8500 & 0.3540 & 0.2332 & 0.2367 bottomrule
 end{tabular}

 end{table*}

 end{document}

The main problem with your table is the unfortunate choice of 6.5 to format the 8 numerical columns; it should be 1.4 throughout. A second issue is that you employ a tabular* environment but give LaTeX no chance to achieve the desired overall width (here: linewidth). Finally, there are only 8, not 9, columns of type d.

documentclass[conference]{IEEEtran}
IEEEoverridecommandlockouts

usepackage{booktabs}
usepackage{dcolumn,tipa}
newcolumntype{d}[1]{D{.}{.}{#1}} % let the 'd' column type take an argument
%usepackage{siunitx}             % not needed for this example
usepackage[usestackEOL]{stackengine}
usepackage{multirow}
newcommandmcc[1]{multicolumn{1}{c}{#1}} % handy shortcut macro

begin{document}

begin{table*}[ht]
caption{Table example}
label{tab1}
%%centering % redundant
%%renewcommandfootnoterule{kern -1ex} % What is this instruction doing here??
renewcommand{arraystretch}{1.3}
setlengthtabcolsep{0pt} % make LaTeX figure out the intercolumn separation
begin{tabular*}{linewidth}{@{extracolsep{fill}} l *{8}{d{1.4}} } % '1.4', not '6.5'
toprule 
multirow{3}{*}{Subjects} & multicolumn{4}{c}{Numbers} & multicolumn{4}{c}{Numbers}
cmidrule{2-5} cmidrule{6-9} &
mcc{XYZ} & mcc{addstackgap{stackanchor{XYZ}{(Numbers)}}} & 
mcc{Numbers Tree} & mcc{Numbers Tree} & 
mcc{XYZ} & mcc{addstackgap{stackanchor{XYZ}{(Numbers)}}} & 
mcc{Numbers Tree} & mcc{Numbers Tree} 
midrule 
X1 & 0.5000 & 0.4888 & 0.0112 & 0.0001 & 0.8500 & 0.3540 & 0.2332 & 0.2367  
X2 & 0.5000 & 0.4888 & 0.0112 & 0.0001 & 0.8500 & 0.3540 & 0.2332 & 0.2367  
X3 & 0.5000 & 0.4888 & 0.0112 & 0.0001 & 0.8500 & 0.3540 & 0.2332 & 0.2367  
X4 & 0.5000 & 0.4888 & 0.0112 & 0.0001 & 0.8500 & 0.3540 & 0.2332 & 0.2367  
X5 & 0.5000 & 0.4888 & 0.0112 & 0.0001 & 0.8500 & 0.3540 & 0.2332 & 0.2367 
bottomrule
end{tabular*}
end{table*}
end{document}