I installed texlive 2013 today. After installation, luatex cannot generate ligatures for "fi fl ff", but it can for ``` '' ---.xetex` works perfectly here, after update.
MWE:
\documentclass{article}
\usepackage{fontspec}
\setmainfont[Ligatures={Common,Rare,TeX}]{EB Garamond}
\begin{document}
\Huge{ffi fl fi `` '' ---}
\end{document}

UPDATE: I tried to use the method described here:
How to enable ligatures for emdash/endash in LuaTeX ?
And luatex can generate ligatures correctly. So is my problem related to fontspec?

xelatexto compile MWE. Still waiting for the update. – capsensitive May 11 '13 at 09:28~/.texlive2013/texmf-var/. This forces the cache to be rebuilt (manually calling luaotfload-tool didn’t do the trick). – georgd May 11 '13 at 12:32