<xsl:variable name="anchor" as="element()*"
   select="document('source.xml')//anchor[parent::xref]/@id"/>

    How can I get all the id values that are not unique?

It's best to say explicitly if you want an xpath2 solution (which you
do here as you are using an as= attribute so you must be using xslt2)

If you just want the distinct values, rather than a sequence of
attribute nodes with distinct values then uou can go

<xsl:variable name="anchor" as="xs:string*"
select="distinct-values(document('source.xml')//anchor[parent::xref]/@id)"/>

Your original as= attribute would generate errors as you are selecting
attribute nodes but specifying a sequence of elements.

Rather than testing on parent:: axis it's probably more natural (but
equivalent) to write this as

<xsl:variable name="anchor" as="xs:string*"
select="distinct-values(document('source.xml')//xref/anchor/@id)"/>

Depending on what you want to do with this list you may prefer to use an
xsl:for-each-group rather than use  distinct-values.

David

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