I don't know the answer to your question however, when a CTR or a SAR is filed, you are required to chose either FinCEN Report 112, which is the form for a CTR, or FinCEN Report 111, which is the form for a SAR. Those documents look very different in length and content. The first page of each report also indicates which BSA document it is. There is no place on a CTR to provide the information that is required for a SAR, so I can't think of any way in which your BSA officer could have filed a SAR on a CTR form.
Is is possible that the confirmation data you observed was linked to completed CTRs instead of completed SARs? Perhaps the wrong BSA confirmation numbers were recorded in the wrong place? Are there saved copies of the actual reports for you to review? Also, is your e-filing done as discrete or as batch filing? We only file discretely, so I have no experience to share about batch filing, which may look different when processing CTRs and SARs.