Calibre shouldn't be doing anything to screw those characters up. The most likely cause is that they're not supported in the font your Kindle software is using.
Try reading the mobi file in Calibre and Kindle for PC to see if the characters show up.
Here are some Kindle test books you can use to verify:
http://freekindlebooks.org/Unicode/unicode.html
You could also try using the 'transliterate unicode characters to ascii' option under look and feel - that function may be smart enough to turn the fractions into vulgar ones.