This bug arises when adding two references to an article that are identical in everything but their name, such as:
<ref name="Name1">Foobar</ref><ref name="Name2">Foobar</ref>
In this circumstance, the references ought to display as one to the reader, since they display exactly the same. However, the software does not do so the same way it does when everything including the name is the same.
This can be resolved by changing the reference names to match, but it should still be fixed, as editors might neglect to do so. It also presents a currently insurmountable issue for uses of the Wikidata module as I explain here, where the reference name is generated and it often would not be advisable to change other instances of the reference supporting separate facts to the generated name.