The \footnote
command is fragile, so that simply placing the
command in \section
's arguments isn't satisfactory. Using
\protect
\footnote
isn't a good idea either: the arguments of a
section command are used in the table of contents and (more
dangerously) potentially also in page headings. Unfortunately,
there's no mechanism to suppress the footnote in the heading while
allowing it in the table of contents, though having footnotes in the
table of contents is probably unsatisfactory anyway.
To suppress the footnote in headings and table of contents:
\section[title]{title
\footnote
{title footnote}}
\footnote
automagically disappear in a moving argument.