Font-family and line- height

I’m not sure if this is the right forum to post this question but I’m having trouble concerning line height. I’m trying to create an app containing footnotes and referances. If the line height for the body text is not specified, (left blank) the line heights looks equal whether the line contains footnote/reference marker or not. But when I specify the line height, the line with the footnote/reference marker gets wider than other lines. Is there any work around on this?