Appleton accused Millwall of taking "cheap shots" at his players after they emerged battered and bruised from the goalless FA Cup quarter-final at The New Den.
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 Danny 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."