I took a look a the filetypes using assoGiate, which clearly shows the problem. 
The mimetype application/x-font-otf doesn't have the filename pattern defined, 
while the application/vnd.oasis.opendocument.formula-template (which is the 
problematic MIME here) does have the filename pattern.
The easiest workaround is as follows: Install and run assogiate (package is in 
universe), find the application/x-font-otf type and edit it, at the filename 
tab add pattern *.otf.
I am not sure how to create regular formula template, but when I change 
extension of some formula document (*.odf) to .otf, it gets detected as 
OpenType font too, but since I almost never work with OpenOffice formulas this 
is not a big deal for me.

As you can see, this problem is clearly MIME related, now it depends
whether the problem is in gnome-mime-data or shared-mime-info.

-- 
OpenType Fonts associated as ODF Template Files
https://bugs.launchpad.net/bugs/338682
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