Scott Dann had his head bandaged after being caught by Rob Hulse's elbow in the first half and he was clattered in the head again in the second by Millwall defender Danny Shittu during a feisty clash in south-east London.
Referee Martin Atkinson dished out seven yellow cards in total with one of the worst offences committed by Shane Lowry, who sent David Bentley flying up in the air with a hefty tackle in the second half.
Bradley Orr came on in the first half for Adam Henley after he suffered an injury, but he himself had to be replaced 12 minutes later with a suspected broken rib following a challenge with Shittu.
"There were a lot of tackles flying around today [Sunday] and a couple of cheap shots going on out there, which is disappointing," Appleton said in his post-match press conference.
"Adam looks as if he has done his hamstring again, which is disappointing.
"Brad might have cracked a rib. He is really struggling with his breathing at the minute and is in a lot of pain.
"He is taking a lot of pain killers and we will get him scanned and X-rayed as soon as possible."
Appleton thinks Wednesday's replay will not be as physical, if the game is officiated by a "strong referee".
"As long as we get a strong referee on Wednesday I don't see there being any problem," Appleton said.
"There were a few arms flailing but that is part and parcel of the game."
Appleton appeared relieved to get through the match unscathed after being forced to field a patchwork team due to injury problems.
He said: "I was delighted with the way the lads went about it. I had three or four players who were only 60-70 per cent fit and we've got another chance to get through.
"It's always going to be (a battle) when you come to the Den with the Millwall fans behind them.
"It was difficult because the ball was changing hands that many times, I'd be surprised if there were three or four (consecutive) passes in the whole match.
"The game on Wednesday is going to be a completely different game."
Appleton also confirmed that Danny Murphy had been formally relieved of the club captaincy, with Scott Dann his replacement, but would continue to be available for selection.
Millwall hit back at Appleton's claims on Sunday evening, insisting they were not overly physical.
"Cheap shots? I don't think that was the case," Millwall boss Kenny Jackett said.
"I don't think that was my players at all."
Lions midfielder Jack Smith reacted angrily to Appleton's comments.
He said: "I didn't see any cheap shots. They seemed to fall over if we breathed on them."
Millwall had a few decent chances, but they were unable to beat Jake Kean in a match that was devoid of any real quality.
Andy Keogh struck a post in the first half, Hulse missed a sitter from six yards after the break, and frontman Dany N'Guessan was poor throughout.
Jackett, who lost Arsenal loanee Benik Afobe to a serious knee injury in midweek, admits his forwards were not up to scratch.
"Goalscoring has been a problem for us in 2013," the Millwall boss said.
"The win was there for us. It is frustrating. In 2012 it wasn't a problem for us, but I think today [Sunday] showed that when we do get on top of sides, we need to score and we didn't.
"There was no lack of passion from the players, but we didn't finish. It's something that we need to improve."
The poor state of Millwall's efforts up front were summed up by the fact that their best chance came from the right boot of 32-year-old centre-back Danny Shittu.
The Nigerian unleashed a powerful 40-yard shot which Kean did well to tip over the bar.
Shittu, who scored in the fifth-round win over Aston Villa, almost scored again soon after with another piledriver.
"If that had gone in, I think I'd have gone straight to the changing room and taken my top off," he said.
The replay will take place on Wednesday night but Shittu, who went as close as anyone to breaking the deadlock with a stunning effort from nearly 40 yards, feels the Lions would have been worthy winners on Sunday afternoon.
"We're disappointed because it was a game we dominated all the way through. It's disappointing not to win," he told ESPN.
"But from the performance today [Sunday] we definitely believe we can go there and get to the semi-finals.
"With the result today [Sunday], and a clean sheet, we can go there and carry on."
Reflecting on his own audacious attempt to beat Jake Kean from just inside the Blackburn half, he added: "If that had gone in, I think I'd have gone straight to the changing room and taken my top off."