It seems like a bug for CkEditor and Footnote macro. You should report it
on https://jira.xwiki.org
You could manually set the footnotes from Wiki syntax, see
http://extensions.xwiki.org/xwiki/bin/view/Extension/Footnote%20Macro
http://extensions.xwiki.org/xwiki/bin/view/Extension/Put%20Footnotes%
I have a page:
==section 1==
==section 2==
footnote
==section 3==
==references==
the footnote is given in section 2.
after editing a whole page footnote reference is auto inserted at page
bottom.. i.e. ==references== here.
this is what i want.
but when i edit the section 2 only (not whole p