[?] added in Kindle

I have some books I have downloaded in mobi format and added to Calibre. I have then copied the books to a basic (not touch-screen) Kindle.

The books look fine in the viewer built into Calibre but when I open the books in the Kindle there are many [?] (squares with a question mark inside) and if I open them in FBReader there are many [] (empty squares).

I think it is mostly where there could be quotation marks - but they are not there in the viewer - and I am not completely sure that the squares are at the exact same places in the Kindle and the FBReader.

What can be wrong and what can I do to fix it ?