Leeds suffered a 1-0 defeat to QPR away from home at Loftus Road in the Championship.
Charlie Austin’s goal in the 58th minute proved to be the difference between the two teams in London.
Former Leeds striker Whelan was far from impressed with Steve Evans’s side's performance, claiming that they lost the midfield battle.
The former Middlesbrough and Derby County man was also appreciative of Rangers striker Austin.
"For me we lost the midfield battle,” Whelan told BBC Sport. "It’s crucial in games like this, especially on a tight pitch
"They were stronger and more aggressive. They have a goal scorer who stays in the goal area and that makes him dangerous.
"I didn't feel we won the midfield, we didn't create enough chances, we didn't defend properly when it came to the crucial goal...
"You have to have your best defender marking their best player, and that's Charlie Austin. They had Charlie Taylor marking him - come on! This is professional football. It should have been organised and you should be able to adapt to the situation.”
Over the course of the 90 minutes at Loftus Road, hosts QPR had 52% of the possession, took 20 shots of which four were on target, and earned eight corners.
Visitors Leeds had 48% of the possession, took seven shots of which just one was on target, and earned one corner.
The West Yorkshire outfit are now 17th in the Championship table with 19 points from 18 matches, just four points above the relegation zone.