I had files with win-1251 encoding. These files were shown as «binary» in web-interface. That is not a problem per se, since we can define binary file as «file which is not UTF-8 compliant».
The problem appeared when I converted these files to UTF-8. For this commit these files are listed in the list «Files changed», but differences for the files are displayed as «File contents unchanged». That can make me think that files are really not changed.
Moreover, for one short file the differences were displayed, and they look like that I changed readable to non-readable text (but in fact I changed non-readable to readable).
P.S. In SourceTree differences are displayed correctly.