renewcommand{@pnumwidth}{<Required-Length-to-Fix-the-Problem>}

documentclass{article}

begin{document}

tableofcontents

pagenumbering{arabic}
setcounter{page}{999}
section{Page numbering using Arabic numbers}
subsection{We can see that 999 is right-aligned as expected}

newpage

pagenumbering{Roman}
setcounter{page}{999}
section{Page numbering using Roman numbers}
subsection{We can see that CMXCIX is not properly aligned}

end{document}

documentclass{article}

makeatletter
renewcommand{@pnumwidth}{5em}
makeatother

begin{document}

tableofcontents

pagenumbering{arabic}
setcounter{page}{999}
section{Page numbering using Arabic numbers}
subsection{We can see that 999 is right-aligned as expected}

newpage

pagenumbering{Roman}
setcounter{page}{999}
section{Page numbering using Roman numbers}
subsection{We can see that CMXCIX is not properly aligned}

end{document}