What version of Sigil?
Were you generating the standard table of contents or an HTML table of contents?
I gotta be honest... I don't think Sigil had anything to do with the "<p><a id="link3"></a></p>" bit regardless of which TOC you were generating. I would hazard a guess that the <p> line isn't necessary, but without seeing the whole ebook, it's impossible to know for sure what else—if anything—might be dependent upon on that "link3" anchor.