The English side was criticized after nine of its players surrounded referee Bjorn Kuipers to persuade him to punish Paris Saint-Germain striker Zlatan Ibrahimovic for fouling Oscar during a Champions League game on Wednesday.
Ibrahimovic, who was given a straight red card, described the Chelsea players as "babies" for their reaction.
The only time Chelsea has been charged this season for failing to control its players was after the 1-0 win over Everton in the Premier League last month. Late in that game, Chelsea's players reacted to a foul on Willian, and Branislav Ivanovic escaped punishment for appearing to wrap his arm around Everton midfielder James McCarthy's neck.
"If they surround the referee, we are charged," Mourinho said, defending his team. "We have at this moment eight or nine months of competition, we were charged once."
Mourinho said his players paid the previous fine of 30,000 pounds ($44,000).
Chelsea captain John Terry said after the game against Paris Saint-Germain, which finished in a 2-2 draw that qualified the French team for the quarterfinals, that badgering the referee is "part of the game."
"It's there and you have to stick up for your teammates," said Terry, who led the protests against Ibrahimovic. "The fans want to see that and that's the same with every side. Every other side is as bad as each other."
Mourinho wouldn't comment any further about the incident Friday.
Chelsea goes into Sunday's match against Southampton holding a five-point lead in the Premier League and with a game in hand.
"For many months, we played better than everyone. In that moment, you were all saying Chelsea was a candidate to win the Champions League," Mourinho said. "We cannot play fantastic all season and we had our lowest point in a moment we couldn't have. We lost the game (against PSG), we are out of the competition."