While their opponents were celebrating moving to the brink of the 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 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."
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."
Sean Dyche lauded his Burnley side for clinching three points in a toxic atmosphere.
Dyche said: "It is another part of the business we have taken care of, it's a big result. That's 11 away (games) unbeaten and we had to work hard.
"There is a lot going on at this club (Blackpool) and we had to stay focused on us because it might go off us on to other things. I thought the players did that well."
Dyche, who admitted he would not go out of his way to watch the final stages of the Rams' trip to Yorkshire, may be keen to keep a lid on any promotion celebrations until it is mathematically certain but even he was willing to praise the 86 points his side have accumulated so far this term.
Malky Mackay's Cardiff won the Championship with just one more point last year and Dyche knows it is a huge achievement for his small squad to almost match that feat.
"Two points a game is a strong marker," he admitted.
"I spoke to Malky and they finished with 87, so to get 86 with three (games) to go is a powerful message about what we've done and what we're doing. But it's still a so-far story."
Even once Burnley's return to the top flight is confirmed, Dyche will not be popping the champagne corks straight away.
The victory moved the Clarets four points behind leaders Leicester, who have not won since their promotion was confirmed.
"The focus has never changed," Dyche added.
"The interesting thing is Derby have changed from 'we're in the play-offs' to 'we could still beat Burnley'.
"If you think of my mantra, it's never changed. Just 'one game at a time', and it's authentic. The next game comes around Monday."