In the aftermath of Michael Kightly's match-winning goal, hundreds of tennis balls were thrown onto the pitch in protest of chairman Karl Oyston's running of the club during their slide down the table.
Ferguson has refused to criticise the supporters who took part in the incident, but did admit that it would be less of a distraction if they were to not demonstrate during play in the future.
"The fans have got every right to demonstrate if they don't like the chairman or the board," Ferguson told reporters.
"I would just rather they do it before the game or after the game. At that stage, we were on top of them. It doesn't affect me. The fans have been great with me and showed their support for the boys."
Blackpool play relegation rivals Millwall in their next Championship fixture on Monday.