City boss Pep Guardiola had coins thrown at him protesting a disallowed goal in their 1-0 loss to Liverpool at Anfield while the hosts later released a statement condemning "vile chants" relating to stadium tragedies.
Ahead of Thursday's League Cup fourth-round meeting between the heavyweights, both teams wrote to their fans urging them to report any inappropriate behaviour.
"It's really positive that both clubs are cooperating. It was a good statement and it was really clear.
"I worked at Porto for seven years the rivalry between Benfica and Porto was on a different level," Lijnders told reporters.
"Playing against City has this importance but with rivalry comes emotion and that's good because we need emotion from our fans and players and they feel like the games matter. The problem with emotion is that there needs to be respect.
"It's not a problem specific to the clubs, it's a football problem."
Guardiola, who previously said City's rivalry with Liverpool was not toxic, told reporters on Wednesday the players, managers and fans wanted to behave but that emotions sometimes got the better of them.
"People can't behave ice-cold when a goal is disallowed when it should be a goal in this type of game. We'll always react in that way, but respect for officials, rules and opponents is always there, from my point of view," Guardiola said.
Lijnders said winger Luis Diaz (25), who is nursing a knee injury after experiencing discomfort in Liverpool's mid-season training camp in Dubai, was in good spirits.
"We all know the impact that Luis Diaz had on the team and it's not easy to come in and have an impact to take the team forward," Lijnders said.
"He has this character where he smiles and works hard and will come back stronger, and that will really help us. Hopefully he'll come back in the shortest time-frame."
