The third subsection in the second subsection of the first section should be numbered 1.2.3. This holds also for RTL languages, since numbers, including Dewey numbering is still LTR even in an RTL language. Babel seems to have this right, but polyglossia is confused. How do you fix that?
Here is an example:
\documentclass{article}
\usepackage{polyglossia}
\setmainlanguage{hebrew}
\setotherlanguage{english}
\newfontfamily\hebrewfont[Script=Hebrew]{Ezra SIL}% or{SBL Hebrew}
\begin{document}
\section{1st Sect. Should be \#1}
\subsection{1st Subsect. Should be \#1.1}
\subsubsection{1st Subsubsect. Should be \#1.1.1}
\subsubsection{2nd Subsubsect. Should be \#1.1.2}
\subsection{2nd Subsect. Should be Numbered 1.2}
\section{2nd Sect. Should be \#2}
\subsection{1st Subsect. Should be \#2.1}
\subsubsection{1st Subsubsect. Should be \#2.1.1}
\subsubsection{2nd Subsubsect. Should be \#2.1.2}
\subsubsection{3rd Subsubsect. Should be \#2.1.3}
\subsection{2nd Subsect. Should be \#2.2}
\subsubsection{1st Subsubsect. Should be \#2.2.1}
\subsubsection{2nd Subsubsect. Should be \#2.2.2}
\end{document}