The issue arose from the production sale of pedigree-registered Ballylinney Beef Shorthorns by Derek and Cindy Steen, Whitcastles Farm, Lockerbie, in March 2015.
BCMS has deregistered a number of the cattle and invalidated their passports after discrepancies over birth dates and disease testing came to light.
It is believed a number of buyers around the UK and Ireland have been affected.
BCMS has sent letters to affected farmers explaining the situation.
Mr Steen denied any wrongdoing and blamed the Scottish livestock movement database for the discrepancies.
He said: “The dates of birth of the cattle are entirely correct. The issue is with the dates which appear on the ScotEID website as to when the cattle were tested for BVD. They are not correct.”
He said he did not want to comment further as his legal representatives were looking into the issue but was confident he would ‘be shown to have done nothing wrong’.
Beef Shorthorn Society president John Riby said: “After the sale it appeared there were irregularities between the birth dates and information on some of the disease testing.
“BCMS was made aware of these discrepancies and we have carried out a thorough investigation. We have had a disciplinary committee meeting and we had Derek Steen available to answer questions and comment.
“There will be a council meeting on May 3 when presumably we will reach a decision on what we are going to do.”
It is believed some of the buyers are seeking legal advice although it is not yet clear what the implications are for the affected cattle and their offspring of the passports being invalidated.