EDIT: This has been fixed in microtype version 3.0a.
Beginning with version 3.0, microtype applies some patches to improve protrusion at "inner margins", e.g. inat the beginning of \items (see chapter 9 of the microtype doc). This requires some gymnastics, and here the active character from csquotes interferes in a bad way. A quick fix would be to prevent the patching with microtypesetup\microtypesetup{nopatch=item}, either for the whole document or only the problematic case. A better fix (which will be included in the next version) would be to patch the pertinent microtype command:
\documentclass{article}
\usepackage{microtype}
\usepackage{csquotes}
\MakeAutoQuote{“}{”}
\usepackage{etoolbox}
\begin{document}
\begin{itemize}
\microtypesetup{nopatch=item}
\item “foo” some more text\\ “another quote”
\end{itemize}
\makeatletter
\patchcmd\MT@get@prot{\noindent}{\noindent\@disablequotes}{}{}
\makeatother
\begin{itemize}
\item “foo” some more text\\ “another quote”
\end{itemize}
\end{document}
(In a real document, you'd move the \MT@get@prot patch to the preamble, of course.)
