"Footnotes appear on-screen in the document margin and at the bottom of the page when printed. You'll be able to see how the footnotes will appear when printed by selecting Print (Ctrl+P) or Download file as... PDF from the File menu. There will also be a footnote marker within the actual document designated by a pound sign (#). You can drag and drop a footnote anywhere you'd like in the document by simply clicking on this pound sign and dragging," notes Google's help page.
Google did a good job at integrating footnotes in the interface, but they should be displayed at the bottom of the page and they should be numbered. Unfortunately, Google Docs still doesn't support pagination.
Another compatibility issue is that word processors will display footnotes as endnotes, at the end of your document.