Vlahos was allegedly bashed at his Torquay property on Sunday night and his car set alight.
Webster said BC3 had been buying horses at Inglis sales for the past five or six years and had shown no signs of financial distress.
"But this is a case where a person was involved in other activities that were completely inappropriate. We had no knowledge of Bill's other life," Webster told Melbourne's RSN radio.
He confirmed Inglis had removed horses in which it held a financial interest from Vlahos's property following the alleged car torching and relocated them to "a safe place".
BC3's most high-profile deal involved a A$5 million half brother to Black Caviar which went through the ring at the Inglis Easter Sale.
Webster confirmed the colt had not been fully paid for by BC3.
The two-year-old colt, known as Jimmy, has since contracted the life-threatening hoof disease laminitis.
BC3 also has a full sister to the colt, Belle Couture, who won a jump-out at Flemington last week in preparation for a planned racetrack debut later this month.
Webster said Inglis would review its business to see if people were able to buy horses too easily under the current structure.
"The challenge for the industry is that it depends on a certain number of horses coming through the system every year and if auction houses are doing the role providing credit to buy horses, that needs to be recognised," he said. "We're going to review our procedures to see if we are being too generous."
It has also been revealed some members of the Victoria Police are among those caught up in the collapse of the punting club.
Chief Commissioner Ken Lay says the Fraud Squad is now investigating the matter.
"This is a dynamic investigation, there's things happening on a daily basis," Lay said.
- AAP
