Using the .fo stylesheets, glossseealso generates a duplicate id when pointing to a glossterm that contains an indexterm. According to an analysis by Bob Stayton, this happens because "glossseealso is handled as a cross reference, and the targets of any cross reference should be processed in mode="no.anchor.mode". That mode prevents the inclusion in the link text of nested links and indexterms. Since that mode is not currently used for glossseealso, the link text includes a duplicate marker for the indexterm included in the glossterm."
I've attached an example of a glossary that will trigger this problem. The example was generated by Dark.Rider85, who discovered the problem.
This was triggered by an indexterm in the glossterm. I changed the processing of xrefs to glossterms to use the no.anchor.mode, which turns off indexterms and nested links.