The Colombian was substituted in the 59th minute of Fulham's shock 1-0 loss to Sheffield United in the FA Cup on Tuesday.
Rodallega said the decision to take him off, to a chorus of boos, was shattering and hinted at a problem with Meulensteen, who took over as manager in December last year.
"I have no relationship with the new manager and I think he has been disrespectful to me," Rodallega told Colombian TV.
"He always keeps his forwards on, whether or not they are playing well, so I don't know why he has done this to me. It broke my heart.
"I've never gone through a situation like the one on Tuesday in my whole career. I couldn't sleep that night. I've had a good career with no acts of indiscipline anywhere.
"But at that moment I felt rage because I wanted to keep playing."
Ahead of returning to Manchester United, where he worked as a youth, reserves and assistant coach, Meulensteen said there was no problem with Rodallega.
"I spoke to Hugo and there is absolutely no issue there at all," he said on Friday.
The dispute is an unneeded distraction for Fulham, who have lost four straight English Premier League matches and are bottom of the table.
Meulensteen rubbished suggestions Alan Curbishley, Fulham's technical director, was in line to take over as manager in their relegation battle.
"It's absolute nonsense," Meulensteen said.
"He has been brought in by myself as a member of the backroom staff as it is good to have that sort of experienced people around you, especially in this important period.
"We have very good co-operation together. He is very helpful. Alan has said, 'make sure that you keep believing in the right things.'"
