[SOLR-5772] duplicate documents between solr "block join" documents and "normal" document - ASF JIRA
I have seen the same issue myself as I started to make use of nested documents. The only way to ensure uniqueness (when updating) is to always have a sub-document even if this does not reflect your data.
This is especially inconvenient since the "empty" child document must have an id field since it is a required field.
I also found this unanswered StackOverflow post that shows another user seeing this bug:
Read full article from [SOLR-5772] duplicate documents between solr "block join" documents and "normal" document - ASF JIRA
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