This is not a bug - it's a feature that I either need an effective work around or I need to write a suggestion.
The letters of Damian are given labels such as {Label Personal Letter WHERE Author ~ <Biography Peter Damian> AND Date ~ <Date 1040 – 1041> AND Recipient ~ "Honestus"}. Notice that Bible references and topics are missing. Given the manual work required to identify those values, I agree that this omission is reasonable.
So I went to select a letter and create a Passage List. Unfortunately, this failed because the references are in the footnotes, not beside the quotation in the letter text. Is there a way to generate a Passage List from references in footnotes?