When reference group names are used, e.g.
content with a footnote<ref group="footnotes">some text</ref> [...] <references group="footnotes" />
the reference will show up as:
content with a footnote[footnotes 1]
(the square brackets are of course in superscript, I just don't know how to do this in the markup). See https://www.mediawiki.org/wiki/Extension:Cite#Grouped_references for the working example.
However, it is currently not possible to use the grouped references without having the group name in the reference text. A usecase for this could be to have the references grouped per paragraph or table.
This feature can be easily implemented by introducing a variable like $wgCiteShowGroupNames which is by default true, but users could overwrite it in the LocalSettings.php. Only if this variable is true, the name of the group is displayed.
A patch for those changes is attached.