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 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."