This bug has been reported in the Debian BTS: http://bugs.debian.org/243283

"I have a file call links.html, which contains XHTML 1.0 (it even
validates). Nautilus looks at the filename and deduces that its type is
"text/html" and the contents and deduces the type as "text/xml". If I
double click on the file, since the types are different, it then pops up
an error dialog saying that I can't open it, there is a security problem
(the actual text is in Finnish, due to my locale; I can reproduce it in
English it if is vital).

This is quite annoying. I have no intention of renaming all my web pages
because of Nautilus."

This is due to the difference between the extension/mime which is html and
content/mime xml.  

There should be a way to turn off the warning displaying for some types or to
specify several mimetypes than an extension can fit.