Fixing importing errors

Footnotes should likely require building a "footnotes" paragraph style. Apply it under Type > Document Footnote Options...

Hyperlinks will often be constructed as a Character Style. If you look, you might already have one in that panel. Not sure based on your comments, but you might have to go thru the document looking for hyperlinks and apply the character style. 

Window > Interactive > Hyperlinks will show you whether your hyperlink urls are live or not. If not, click on the Hyperlinks panel menu button ( ) and choose Convert URLS to Hyperlinks

Did you select "show options" when placing the document? If not, go back and do it that way.