that square indicates that the BOOK used a glyph that is not available on YOUR device (or the font that may have been embedded )
2 choices come to mind;
1)Embed the proper font (
Personal use only for many fonts) with all the needed glyph's (the font you have, may have been subsetted incorrectly)
2)Use the ebook Editior to Search that 'box' and Replace with a more common one.

The 'character' tools Icon looks like intersecting black and white walls. That can be use to insert where the Insert cursor is (like in Replace

)