Rovers manager Michael Appleton accused the Lions of taking "cheap shots" at his players after a bruising 0-0 draw in the original tie on Sunday, which left Scott Dann with a bandaged head and Bradley Orr a damaged rib.
But midfielder Trotter was in the thick of the action and insisted his team played hard but fair, with a Wembley semi-final against Wigan awaiting the winners, and he said: "It's always physical, football is a contact sport. I thought it was a fair game and the referee did really well. I didn't see any cheap shots."
He added: "Collisions happen in football. I think Bradley Orr collided with Dan Shittu - and those sorts of things are going to happen if you collide with Dan!
"I'm surprised but that's their manager's point of view. From being out on the pitch I thought it was a very fair game between two competitive teams.
"We want to get to Wembley, we realise how important it is to the fans and to the club, but we are focused on playing our normal game against a club in the same league as us.
"We've got every chance of beating them, we have already beaten them at Ewood Park this season and we plan to do the same again.
"It's going to be a difficult game and we have to maintain the performance from Sunday, and if we do that we'll give ourselves a good opportunity. I'm sure they are thinking of tactics and plans to adapt to the way we played on Sunday so it all could change, but we have to do the basics right."
Trotter is only 24 but has already played, and won, at Wembley twice. He was in the Millwall team which beat Swindon in the 2010 League One play-off final - 12 months after helping Scunthorpe sink the Lions on the same stage.
"I've been very lucky," he added. "I'm relatively young and I've been to Wembley twice and both times won the game and got promoted - once against these guys, unfortunately for them. It's a great stadium, a great atmosphere and it's great for your family and friends. But we are focused on Blackburn and winning the game in front of us."