An unused reference in a research paper
This depends on the journal's style sheet, but usually you only list the references that are cited in the text. Thus, I would delete the superfluous ones (and renumber the notes).
It depends on why those "references" were present in the first place. If they're mistakes, get rid of them. If you want to point your readers to additional information, put them in a section called "Further Reading" following the References section. The style of the publication may dictate whether and exactly how you do that, but those dangling references do not belong in the References section.
You have three options. I would consider any of them valid, but an editor might disagree.
Remove the extra references and renumber if necessary.
Put a note somewhere, say with the bibliography, that some references here are just background.
Ignore the problem, assuming that readers will assume 2.
I think these are in order of decreasing preference, but I wouldn't object to any of them.