I experienced the following issue on contrib.xwiki.org: the page is declared on XWiki Syntax 2.0.
I started to edit it in Wiki mode, adding a link with an anchor by following XWiki Syntax 2.1:
I saved it and saw that the links wasn't working (the anchor wasn't followed).
I edited the section in WYSIWYG mode, but switched it to source mode: it displayed the following:
I finally came back on WYSIWYG mode and edited the link using it, which indeed produced the link with the XWiki Syntax 2.0 (diff can be seen here: http://contrib.xwiki.org/xwiki/bin/view/Main/?viewer=changes&rev1=122.1&rev2=122.2&)
So I think there's an issue in the "source" mode of the WYSIWYG editor which does not always show the real syntax.