While their opponents were celebrating moving to the brink of the Barclays Premier League, the Seasiders were in turmoil.
Shortly after Michael Kightly's winning goal early in the second half, home supporters protesting against chairman Karl Oyston threw tennis balls and tangerines on to the turf while some invaded the pitch as referee Michael Oliver was forced to stop play twice.
Things would only get worse, though, as television cameras captured Malcolm, the former Rangers and Motherwell player, pushing substitute Dobbie in the face as the striker waited to come on to the pitch.
"There is no problem," Ferguson said after the full-time whistle.
"Tensions are a bit high; I have no problem with that. They are both passionate guys."
Dobbie, who also began his career with Rangers, played for Hibs, St Johnstone and Queen of the South.
While Ferguson can claim there is no problem inside the Blackpool dressing room, the acidic nature of the fans' feeling towards Oyston will only increase if Millwall win on Saturday and send the Seasiders in to the Sky Bet Championship's bottom three.
The Scot, who is still adored by the fans despite their slide down the table, claims he understands their frustrations but was disappointed they decided to show their anger during the second half.
"The fans have got every right to demonstrate if they don't like the chairman or the board," Ferguson said.
"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."
The fans' admiration for Ferguson may be born out of his willingness to play in Blackpool's midfield despite needing an operation on his ankle.
However, while he is fighting through the pain barrier, Seasiders top scorer Ricardo Fuller remains sidelined by a knee injury which will keep him out of Monday's meeting with Brighton.
Blackpool have not won a game without Fuller since the ex-Stoke striker made his bow in August, but Ferguson added: "I know what type of character Ricky is.
"He would do it but I am not going to harm him long term.
"He is desperate to try and get back, if not for the Wigan game, then for Charlton."